Starting phenix.real_space_refine on Sat Dec 9 20:17:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/12_2023/6ofe_20043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/12_2023/6ofe_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_20043/12_2023/6ofe_20043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/12_2023/6ofe_20043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/12_2023/6ofe_20043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/12_2023/6ofe_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.67, per 1000 atoms: 0.55 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: 4.83 Conformation dependent library (CDL) restraints added in 2.5 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: 0.91 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: 3.15 Time building geometry restraints manager: 5.14 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: 0.850 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: 4.030 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.210 Find NCS groups from input model: 0.800 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:2.810 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- 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 : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.2431 time to fit residues: 146.0012 Evaluate side-chains 319 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7928 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.5980 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8319 moved from start: 0.2537 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= 0.138 Angle : 0.472 6.501 16940 Z= 0.256 Chirality : 0.033 0.098 1940 Planarity : 0.005 0.024 2220 Dihedral : 3.816 12.948 1680 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.46 % Allowed : 17.00 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.17), residues: 1520 helix: -1.05 (0.11), residues: 1380 sheet: None (None), residues: 0 loop : -3.99 (0.42), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 5 PHE 0.009 0.001 PHE N 16 TYR 0.012 0.001 TYR T 47 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 359 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 340 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 346 average time/residue: 0.2345 time to fit residues: 116.1404 Evaluate side-chains 296 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 291 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2020 time to fit residues: 3.5002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 102 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 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 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 61 GLN B 24 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 61 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12440 Z= 0.157 Angle : 0.441 6.423 16940 Z= 0.232 Chirality : 0.033 0.104 1940 Planarity : 0.003 0.030 2220 Dihedral : 3.637 14.036 1680 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.31 % Allowed : 21.92 % Favored : 76.77 % 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: 0.62 (0.20), residues: 1520 helix: 0.78 (0.13), residues: 1360 sheet: None (None), residues: 0 loop : -2.19 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 5 PHE 0.006 0.001 PHE L 16 TYR 0.010 0.001 TYR N 54 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 330 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 313 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 320 average time/residue: 0.2310 time to fit residues: 106.4975 Evaluate side-chains 292 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 285 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1585 time to fit residues: 3.6356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 0.0570 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 112 optimal weight: 5.9990 overall best weight: 0.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN 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** 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** D 24 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12440 Z= 0.113 Angle : 0.409 5.930 16940 Z= 0.210 Chirality : 0.033 0.097 1940 Planarity : 0.003 0.025 2220 Dihedral : 3.471 14.322 1680 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.15 % Allowed : 22.54 % Favored : 76.31 % 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: 1.95 (0.21), residues: 1520 helix: 1.67 (0.13), residues: 1360 sheet: None (None), residues: 0 loop : -1.87 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 5 PHE 0.006 0.001 PHE D 16 TYR 0.019 0.001 TYR M 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 327 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 312 time to evaluate : 1.424 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 320 average time/residue: 0.2545 time to fit residues: 116.6353 Evaluate side-chains 295 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 288 time to evaluate : 1.471 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1208 time to fit residues: 3.5776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 121 optimal weight: 0.0020 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 26 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 55 ASN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12440 Z= 0.113 Angle : 0.406 6.039 16940 Z= 0.208 Chirality : 0.033 0.096 1940 Planarity : 0.003 0.029 2220 Dihedral : 3.398 14.045 1680 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.00 % Allowed : 23.31 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.21), residues: 1520 helix: 2.23 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.57 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 5 PHE 0.005 0.001 PHE A 16 TYR 0.014 0.001 TYR O 47 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 315 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 302 time to evaluate : 1.424 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 310 average time/residue: 0.2303 time to fit residues: 103.2929 Evaluate side-chains 291 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 282 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1304 time to fit residues: 3.8526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 63 ASN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 26 GLN M 61 GLN O 24 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3519 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= 0.136 Angle : 0.421 5.803 16940 Z= 0.215 Chirality : 0.034 0.101 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.411 14.211 1680 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.92 % Allowed : 23.23 % Favored : 75.85 % 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: 3.20 (0.21), residues: 1520 helix: 2.50 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.62 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.007 0.001 PHE N 16 TYR 0.017 0.001 TYR O 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 315 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 303 time to evaluate : 1.400 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 310 average time/residue: 0.2341 time to fit residues: 104.9833 Evaluate side-chains 295 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 287 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1864 time to fit residues: 4.1050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN N 55 ASN G 24 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN C 24 GLN E 26 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12440 Z= 0.178 Angle : 0.441 5.607 16940 Z= 0.227 Chirality : 0.035 0.102 1940 Planarity : 0.003 0.027 2220 Dihedral : 3.518 15.137 1680 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.85 % Allowed : 23.85 % Favored : 75.31 % 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: 3.22 (0.21), residues: 1520 helix: 2.52 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.71 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 5 PHE 0.005 0.001 PHE G 68 TYR 0.019 0.001 TYR O 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 312 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 301 time to evaluate : 1.496 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 308 average time/residue: 0.2269 time to fit residues: 101.3984 Evaluate side-chains 300 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 294 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1902 time to fit residues: 3.6127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 61 GLN N 24 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 ASN ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN C 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12440 Z= 0.158 Angle : 0.436 5.391 16940 Z= 0.225 Chirality : 0.034 0.101 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.499 15.413 1680 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.08 % Allowed : 24.38 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.21), residues: 1520 helix: 2.65 (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 0.011 0.001 TRP T 5 PHE 0.006 0.001 PHE O 16 TYR 0.022 0.001 TYR O 47 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 319 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 305 time to evaluate : 1.328 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 315 average time/residue: 0.2345 time to fit residues: 107.5784 Evaluate side-chains 302 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 290 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1298 time to fit residues: 4.7525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN N 24 GLN N 55 ASN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3800 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= 0.123 Angle : 0.422 5.301 16940 Z= 0.217 Chirality : 0.033 0.100 1940 Planarity : 0.003 0.029 2220 Dihedral : 3.415 14.796 1680 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.23 % Allowed : 24.92 % Favored : 74.85 % 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: 3.62 (0.21), residues: 1520 helix: 2.82 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.76 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 5 PHE 0.005 0.001 PHE C 16 TYR 0.024 0.001 TYR O 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 308 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 1.255 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 306 average time/residue: 0.2122 time to fit residues: 95.2878 Evaluate side-chains 288 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1384 time to fit residues: 1.9343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 0.1980 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN N 24 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3849 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= 0.133 Angle : 0.432 6.906 16940 Z= 0.222 Chirality : 0.034 0.097 1940 Planarity : 0.003 0.025 2220 Dihedral : 3.383 14.890 1680 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.31 % Allowed : 25.92 % Favored : 73.77 % 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: 3.79 (0.21), residues: 1520 helix: 2.93 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.73 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP S 5 PHE 0.004 0.001 PHE N 16 TYR 0.014 0.001 TYR K 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 296 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 1.293 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 294 average time/residue: 0.2224 time to fit residues: 95.5254 Evaluate side-chains 289 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1621 time to fit residues: 2.0295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN N 24 GLN O 24 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.080761 restraints weight = 21622.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.083090 restraints weight = 11072.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.084610 restraints weight = 6881.191| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12440 Z= 0.148 Angle : 0.442 6.419 16940 Z= 0.226 Chirality : 0.034 0.099 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.406 15.177 1680 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.46 % Allowed : 25.85 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.21), residues: 1520 helix: 3.00 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.75 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP S 5 PHE 0.005 0.001 PHE N 16 TYR 0.015 0.001 TYR S 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: 2546.95 seconds wall clock time: 47 minutes 31.38 seconds (2851.38 seconds total)