Starting phenix.real_space_refine on Sat Dec 9 13:19:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/12_2023/6n1i_8903.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/12_2023/6n1i_8903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/12_2023/6n1i_8903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/12_2023/6n1i_8903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/12_2023/6n1i_8903.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/12_2023/6n1i_8903.pdb" } resolution = 3.58 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 7088 2.51 5 N 1920 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "I ARG 9": "NH1" <-> "NH2" Residue "J ARG 9": "NH1" <-> "NH2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "M ARG 9": "NH1" <-> "NH2" Residue "N ARG 9": "NH1" <-> "NH2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "P ARG 9": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11136 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "B" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "E" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "F" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "H" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "I" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "J" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "K" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "L" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "M" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "N" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "O" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "P" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Time building chain proxies: 7.03, per 1000 atoms: 0.63 Number of scatterers: 11136 At special positions: 0 Unit cell: (84.48, 84.48, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 2016 8.00 N 1920 7.00 C 7088 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 1.9 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.592A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.511A pdb=" N ILE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.832A pdb=" N ASN A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 43 " --> pdb=" O ASN C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN D 22 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D 25 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 25 " --> pdb=" O LYS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS E 43 " --> pdb=" O ASN E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E 57 " --> pdb=" O GLY E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 85 removed outlier: 3.661A pdb=" N PHE E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 7 through 12 Processing helix chain 'F' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN F 22 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS F 43 " --> pdb=" O ASN F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE F 81 " --> pdb=" O ASN F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 7 through 12 Processing helix chain 'G' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS G 43 " --> pdb=" O ASN G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 76 removed outlier: 3.832A pdb=" N ASN G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE G 69 " --> pdb=" O SER G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE G 81 " --> pdb=" O ASN G 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 7 through 12 Processing helix chain 'H' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS H 43 " --> pdb=" O ASN H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET H 57 " --> pdb=" O GLY H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN H 67 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 85 removed outlier: 3.663A pdb=" N PHE H 81 " --> pdb=" O ASN H 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 7 through 12 Processing helix chain 'I' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 removed outlier: 3.511A pdb=" N ILE I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET I 57 " --> pdb=" O GLY I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN I 67 " --> pdb=" O SER I 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE I 69 " --> pdb=" O SER I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE I 81 " --> pdb=" O ASN I 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 7 through 12 Processing helix chain 'J' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN J 22 " --> pdb=" O THR J 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN J 67 " --> pdb=" O SER J 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE J 81 " --> pdb=" O ASN J 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN K 22 " --> pdb=" O THR K 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP K 25 " --> pdb=" O LYS K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE K 41 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 76 removed outlier: 3.834A pdb=" N ASN K 67 " --> pdb=" O SER K 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE K 69 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE K 81 " --> pdb=" O ASN K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'L' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN L 22 " --> pdb=" O THR L 18 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP L 25 " --> pdb=" O LYS L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE L 41 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS L 43 " --> pdb=" O ASN L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET L 57 " --> pdb=" O GLY L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN L 67 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU L 68 " --> pdb=" O GLU L 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE L 69 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 removed outlier: 3.661A pdb=" N PHE L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 7 Processing helix chain 'M' and resid 7 through 12 Processing helix chain 'M' and resid 16 through 30 removed outlier: 4.152A pdb=" N GLN M 22 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET M 57 " --> pdb=" O GLY M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.834A pdb=" N ASN M 67 " --> pdb=" O SER M 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE M 69 " --> pdb=" O SER M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 85 removed outlier: 3.661A pdb=" N PHE M 81 " --> pdb=" O ASN M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 12 Processing helix chain 'N' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN N 22 " --> pdb=" O THR N 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE N 41 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS N 43 " --> pdb=" O ASN N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE N 55 " --> pdb=" O ALA N 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET N 57 " --> pdb=" O GLY N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN N 67 " --> pdb=" O SER N 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU N 68 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE N 69 " --> pdb=" O SER N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE N 81 " --> pdb=" O ASN N 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 7 through 12 Processing helix chain 'O' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP O 25 " --> pdb=" O LYS O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 43 removed outlier: 3.896A pdb=" N ILE O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS O 43 " --> pdb=" O ASN O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE O 55 " --> pdb=" O ALA O 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET O 57 " --> pdb=" O GLY O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 removed outlier: 3.832A pdb=" N ASN O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU O 68 " --> pdb=" O GLU O 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE O 69 " --> pdb=" O SER O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 85 removed outlier: 3.663A pdb=" N PHE O 81 " --> pdb=" O ASN O 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 7 through 12 Processing helix chain 'P' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN P 22 " --> pdb=" O THR P 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP P 25 " --> pdb=" O LYS P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 43 removed outlier: 3.896A pdb=" N ILE P 41 " --> pdb=" O GLU P 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS P 43 " --> pdb=" O ASN P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 59 removed outlier: 3.511A pdb=" N ILE P 55 " --> pdb=" O ALA P 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN P 67 " --> pdb=" O SER P 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU P 68 " --> pdb=" O GLU P 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 85 removed outlier: 3.663A pdb=" N PHE P 81 " --> pdb=" O ASN P 77 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3544 1.34 - 1.45: 1292 1.45 - 1.57: 6284 1.57 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 11296 Sorted by residual: bond pdb=" C TYR P 78 " pdb=" N PRO P 79 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.19e-02 7.06e+03 4.01e+00 bond pdb=" C TYR G 78 " pdb=" N PRO G 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.19e-02 7.06e+03 3.85e+00 bond pdb=" C TYR H 78 " pdb=" N PRO H 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.19e-02 7.06e+03 3.85e+00 bond pdb=" C TYR A 78 " pdb=" N PRO A 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.19e-02 7.06e+03 3.79e+00 bond pdb=" C TYR F 78 " pdb=" N PRO F 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.19e-02 7.06e+03 3.76e+00 ... (remaining 11291 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.84: 138 105.84 - 112.86: 6142 112.86 - 119.88: 3728 119.88 - 126.90: 5017 126.90 - 133.93: 143 Bond angle restraints: 15168 Sorted by residual: angle pdb=" C TRP P 30 " pdb=" N ASN P 31 " pdb=" CA ASN P 31 " ideal model delta sigma weight residual 122.40 127.15 -4.75 1.45e+00 4.76e-01 1.07e+01 angle pdb=" C TRP H 30 " pdb=" N ASN H 31 " pdb=" CA ASN H 31 " ideal model delta sigma weight residual 122.40 127.13 -4.73 1.45e+00 4.76e-01 1.06e+01 angle pdb=" C TRP I 30 " pdb=" N ASN I 31 " pdb=" CA ASN I 31 " ideal model delta sigma weight residual 122.40 127.11 -4.71 1.45e+00 4.76e-01 1.05e+01 angle pdb=" C TRP J 30 " pdb=" N ASN J 31 " pdb=" CA ASN J 31 " ideal model delta sigma weight residual 122.40 127.09 -4.69 1.45e+00 4.76e-01 1.05e+01 angle pdb=" C TRP A 30 " pdb=" N ASN A 31 " pdb=" CA ASN A 31 " ideal model delta sigma weight residual 122.40 127.08 -4.68 1.45e+00 4.76e-01 1.04e+01 ... (remaining 15163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.94: 5900 9.94 - 19.87: 834 19.87 - 29.81: 133 29.81 - 39.75: 61 39.75 - 49.68: 16 Dihedral angle restraints: 6944 sinusoidal: 2960 harmonic: 3984 Sorted by residual: dihedral pdb=" CA LEU J 68 " pdb=" C LEU J 68 " pdb=" N PHE J 69 " pdb=" CA PHE J 69 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LEU B 68 " pdb=" C LEU B 68 " pdb=" N PHE B 69 " pdb=" CA PHE B 69 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LEU A 68 " pdb=" C LEU A 68 " pdb=" N PHE A 69 " pdb=" CA PHE A 69 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 6941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1103 0.048 - 0.097: 497 0.097 - 0.145: 64 0.145 - 0.193: 32 0.193 - 0.242: 16 Chirality restraints: 1712 Sorted by residual: chirality pdb=" CB ILE M 20 " pdb=" CA ILE M 20 " pdb=" CG1 ILE M 20 " pdb=" CG2 ILE M 20 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE A 20 " pdb=" CA ILE A 20 " pdb=" CG1 ILE A 20 " pdb=" CG2 ILE A 20 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE E 20 " pdb=" CA ILE E 20 " pdb=" CG1 ILE E 20 " pdb=" CG2 ILE E 20 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1709 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 78 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 79 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR O 78 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO O 79 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO O 79 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO O 79 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 78 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO H 79 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 79 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 79 " -0.027 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 157 1.90 - 2.65: 327 2.65 - 3.40: 15715 3.40 - 4.15: 26803 4.15 - 4.90: 49850 Nonbonded interactions: 92852 Sorted by model distance: nonbonded pdb=" CD GLN N 48 " pdb=" CG GLU O 36 " model vdw 1.147 3.670 nonbonded pdb=" CD GLN F 48 " pdb=" CG GLU G 36 " model vdw 1.147 3.670 nonbonded pdb=" CD GLN I 48 " pdb=" CG GLU J 36 " model vdw 1.156 3.670 nonbonded pdb=" CD GLN A 48 " pdb=" CG GLU B 36 " model vdw 1.157 3.670 nonbonded pdb=" CD GLN E 48 " pdb=" CG GLU F 36 " model vdw 1.165 3.670 ... (remaining 92847 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' } 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: 0.520 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: 3.150 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.300 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 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 : 0.009 0.072 11296 Z= 0.541 Angle : 1.125 7.903 15168 Z= 0.657 Chirality : 0.057 0.242 1712 Planarity : 0.006 0.048 1920 Dihedral : 9.867 49.682 4320 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -6.04 (0.15), residues: 1328 helix: -4.41 (0.08), residues: 1008 sheet: None (None), residues: 0 loop : -1.36 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP M 30 HIS 0.003 0.001 HIS O 56 PHE 0.018 0.003 PHE I 81 TYR 0.003 0.001 TYR O 78 ARG 0.003 0.001 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 487 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.2351 time to fit residues: 161.0369 Evaluate side-chains 376 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 77 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN C 77 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 HIS F 77 ASN G 31 ASN H 85 ASN J 13 GLN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 ASN ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN O 22 GLN O 77 ASN O 85 ASN ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11296 Z= 0.244 Angle : 0.717 8.215 15168 Z= 0.383 Chirality : 0.043 0.162 1712 Planarity : 0.005 0.043 1920 Dihedral : 5.621 20.417 1424 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.93 % Allowed : 11.71 % Favored : 85.36 % 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: -3.64 (0.19), residues: 1328 helix: -2.56 (0.12), residues: 1120 sheet: None (None), residues: 0 loop : 0.32 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 76 HIS 0.003 0.001 HIS N 56 PHE 0.028 0.002 PHE B 81 TYR 0.012 0.002 TYR B 78 ARG 0.007 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 456 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 467 average time/residue: 0.2244 time to fit residues: 148.0158 Evaluate side-chains 415 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 398 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1014 time to fit residues: 5.1678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN B 39 ASN C 77 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN J 39 ASN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN O 13 GLN O 85 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.9662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11296 Z= 0.283 Angle : 0.726 10.623 15168 Z= 0.379 Chirality : 0.044 0.174 1712 Planarity : 0.005 0.043 1920 Dihedral : 5.194 25.215 1424 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.16 % Allowed : 15.66 % Favored : 81.17 % 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: -2.08 (0.22), residues: 1328 helix: -1.23 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -0.88 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP M 76 HIS 0.004 0.001 HIS D 56 PHE 0.026 0.003 PHE B 81 TYR 0.010 0.001 TYR F 78 ARG 0.015 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 537 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 13 residues processed: 555 average time/residue: 0.2323 time to fit residues: 180.2136 Evaluate side-chains 477 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 464 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1039 time to fit residues: 4.4429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN B 13 GLN C 7 ASN D 77 ASN F 67 ASN ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 1.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11296 Z= 0.179 Angle : 0.570 9.572 15168 Z= 0.300 Chirality : 0.042 0.162 1712 Planarity : 0.003 0.044 1920 Dihedral : 4.764 21.400 1424 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.64 % Allowed : 19.22 % Favored : 77.14 % 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: -1.19 (0.23), residues: 1328 helix: -0.55 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.13 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 76 HIS 0.005 0.001 HIS O 56 PHE 0.025 0.002 PHE P 3 TYR 0.014 0.001 TYR J 78 ARG 0.006 0.001 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 492 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 510 average time/residue: 0.2283 time to fit residues: 164.1189 Evaluate side-chains 479 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 460 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1059 time to fit residues: 5.6322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 0.0050 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN F 48 GLN F 67 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 GLN O 39 ASN ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 1.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11296 Z= 0.167 Angle : 0.560 7.982 15168 Z= 0.292 Chirality : 0.040 0.160 1712 Planarity : 0.003 0.040 1920 Dihedral : 4.539 20.943 1424 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.61 % Allowed : 19.70 % Favored : 77.69 % 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: -0.70 (0.24), residues: 1328 helix: -0.22 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -0.99 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 76 HIS 0.005 0.001 HIS O 56 PHE 0.028 0.002 PHE H 81 TYR 0.017 0.001 TYR E 78 ARG 0.004 0.000 ARG K 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 483 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 9 residues processed: 492 average time/residue: 0.2308 time to fit residues: 162.2498 Evaluate side-chains 469 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 460 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1229 time to fit residues: 3.8930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 82 GLN E 22 GLN E 39 ASN G 22 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN P 85 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 1.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11296 Z= 0.181 Angle : 0.583 8.421 15168 Z= 0.303 Chirality : 0.041 0.156 1712 Planarity : 0.003 0.036 1920 Dihedral : 4.481 20.153 1424 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.14 % Allowed : 21.20 % Favored : 76.66 % 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: -0.52 (0.24), residues: 1328 helix: -0.02 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.39 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 76 HIS 0.005 0.001 HIS O 56 PHE 0.036 0.002 PHE H 69 TYR 0.013 0.001 TYR E 78 ARG 0.006 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 494 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 498 average time/residue: 0.2344 time to fit residues: 163.5704 Evaluate side-chains 475 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 463 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1019 time to fit residues: 4.1461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 7 ASN G 77 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 1.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11296 Z= 0.178 Angle : 0.589 8.282 15168 Z= 0.308 Chirality : 0.042 0.161 1712 Planarity : 0.003 0.038 1920 Dihedral : 4.467 20.014 1424 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.50 % Allowed : 23.42 % Favored : 75.08 % 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: -0.31 (0.24), residues: 1328 helix: 0.14 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.44 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 76 HIS 0.005 0.001 HIS O 56 PHE 0.037 0.002 PHE A 81 TYR 0.027 0.002 TYR A 78 ARG 0.004 0.000 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 499 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 504 average time/residue: 0.2342 time to fit residues: 165.1995 Evaluate side-chains 490 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 481 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1140 time to fit residues: 3.6180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN G 77 ASN H 85 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN O 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 1.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11296 Z= 0.214 Angle : 0.619 8.126 15168 Z= 0.324 Chirality : 0.042 0.165 1712 Planarity : 0.003 0.034 1920 Dihedral : 4.535 21.334 1424 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.50 % Allowed : 23.81 % Favored : 74.68 % 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: -0.21 (0.24), residues: 1328 helix: 0.22 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.52 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 76 HIS 0.005 0.001 HIS O 56 PHE 0.032 0.002 PHE A 81 TYR 0.013 0.001 TYR E 78 ARG 0.008 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 492 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 501 average time/residue: 0.2409 time to fit residues: 166.5334 Evaluate side-chains 481 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 472 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0990 time to fit residues: 3.3717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN E 85 ASN F 7 ASN G 77 ASN H 7 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN P 39 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 1.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11296 Z= 0.186 Angle : 0.619 8.597 15168 Z= 0.325 Chirality : 0.042 0.160 1712 Planarity : 0.003 0.043 1920 Dihedral : 4.555 20.511 1424 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.27 % Allowed : 25.24 % Favored : 73.50 % 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: -0.11 (0.24), residues: 1328 helix: 0.30 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 76 HIS 0.005 0.001 HIS O 56 PHE 0.039 0.002 PHE A 81 TYR 0.020 0.002 TYR B 78 ARG 0.008 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 486 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 490 average time/residue: 0.2417 time to fit residues: 164.8442 Evaluate side-chains 464 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 457 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1016 time to fit residues: 3.2177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 78 optimal weight: 0.0010 chunk 62 optimal weight: 0.1980 chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN F 7 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 ASN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN P 39 ASN P 85 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 1.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11296 Z= 0.185 Angle : 0.638 8.896 15168 Z= 0.335 Chirality : 0.042 0.157 1712 Planarity : 0.004 0.041 1920 Dihedral : 4.595 20.242 1424 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.63 % Allowed : 26.34 % Favored : 73.02 % 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: 0.07 (0.23), residues: 1328 helix: 0.44 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP L 76 HIS 0.006 0.001 HIS O 56 PHE 0.039 0.002 PHE P 81 TYR 0.014 0.001 TYR A 78 ARG 0.011 0.001 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 485 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 486 average time/residue: 0.2434 time to fit residues: 164.3214 Evaluate side-chains 472 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 468 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1251 time to fit residues: 2.7291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 GLN M 31 ASN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 ASN N 31 ASN P 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124795 restraints weight = 16231.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127786 restraints weight = 8027.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129649 restraints weight = 4483.879| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 1.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11296 Z= 0.195 Angle : 0.641 8.831 15168 Z= 0.340 Chirality : 0.042 0.178 1712 Planarity : 0.004 0.045 1920 Dihedral : 4.559 20.120 1424 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.79 % Allowed : 26.27 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.23), residues: 1328 helix: 0.49 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -1.50 (0.34), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 76 HIS 0.003 0.001 HIS O 56 PHE 0.036 0.002 PHE P 81 TYR 0.028 0.002 TYR A 78 ARG 0.010 0.001 ARG A 52 =============================================================================== Job complete usr+sys time: 3038.74 seconds wall clock time: 55 minutes 26.96 seconds (3326.96 seconds total)