Starting phenix.real_space_refine on Fri Mar 15 08:53:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/03_2024/6n1i_8903.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/03_2024/6n1i_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_8903/03_2024/6n1i_8903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/03_2024/6n1i_8903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/03_2024/6n1i_8903.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/03_2024/6n1i_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-dev-5265/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: 6.32, per 1000 atoms: 0.57 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: 4.60 Conformation dependent library (CDL) restraints added in 2.0 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: 1.23 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: 2.74 Time building geometry restraints manager: 4.93 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: 0.740 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: 3.170 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.160 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.990 ------------------------------------------------------------------------------- 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 : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6847 (mtt) cc_final: 0.6619 (mtt) REVERT: A 76 TRP cc_start: 0.5894 (m100) cc_final: 0.5428 (m100) REVERT: C 26 ASP cc_start: 0.5964 (m-30) cc_final: 0.5429 (m-30) REVERT: D 31 ASN cc_start: 0.7305 (m110) cc_final: 0.7101 (m110) REVERT: F 59 LEU cc_start: 0.8843 (mt) cc_final: 0.8286 (mt) REVERT: I 41 ILE cc_start: 0.7969 (mt) cc_final: 0.7743 (mt) REVERT: K 23 ILE cc_start: 0.6799 (mt) cc_final: 0.6424 (mt) REVERT: K 24 THR cc_start: 0.5636 (p) cc_final: 0.5419 (p) REVERT: M 39 ASN cc_start: 0.8245 (m-40) cc_final: 0.7882 (m-40) REVERT: M 49 ASP cc_start: 0.7176 (m-30) cc_final: 0.6920 (m-30) REVERT: O 15 MET cc_start: 0.4758 (ttt) cc_final: 0.4550 (ttt) REVERT: O 26 ASP cc_start: 0.6343 (m-30) cc_final: 0.6053 (m-30) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.2280 time to fit residues: 155.7298 Evaluate side-chains 376 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.7980 chunk 116 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 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 39 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11296 Z= 0.244 Angle : 0.711 7.722 15168 Z= 0.381 Chirality : 0.042 0.169 1712 Planarity : 0.005 0.048 1920 Dihedral : 5.569 20.484 1424 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.09 % Allowed : 10.84 % Favored : 86.08 % 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: -4.00 (0.18), residues: 1328 helix: -2.54 (0.12), residues: 1168 sheet: None (None), residues: 0 loop : -1.07 (0.37), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 76 HIS 0.002 0.001 HIS N 56 PHE 0.029 0.002 PHE B 81 TYR 0.012 0.002 TYR B 78 ARG 0.007 0.001 ARG D 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 490 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 451 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6781 (m-30) cc_final: 0.6089 (m-30) REVERT: B 1 MET cc_start: 0.6278 (tpp) cc_final: 0.5947 (mmm) REVERT: C 80 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7160 (tt) REVERT: D 1 MET cc_start: 0.7329 (tpp) cc_final: 0.7105 (tpt) REVERT: E 3 PHE cc_start: 0.7416 (t80) cc_final: 0.7140 (t80) REVERT: E 37 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6361 (mt-10) REVERT: E 47 GLU cc_start: 0.7273 (pt0) cc_final: 0.6537 (pt0) REVERT: G 38 VAL cc_start: 0.7814 (t) cc_final: 0.7560 (t) REVERT: H 1 MET cc_start: 0.7759 (tpp) cc_final: 0.7540 (tpp) REVERT: I 2 ASN cc_start: 0.6650 (t0) cc_final: 0.6445 (p0) REVERT: J 1 MET cc_start: 0.6220 (tpt) cc_final: 0.5935 (tpt) REVERT: J 26 ASP cc_start: 0.7253 (m-30) cc_final: 0.6780 (m-30) REVERT: K 22 GLN cc_start: 0.7126 (tp40) cc_final: 0.6834 (mm110) REVERT: L 20 ILE cc_start: 0.7335 (tt) cc_final: 0.6966 (tt) REVERT: M 36 GLU cc_start: 0.6140 (mp0) cc_final: 0.5915 (mp0) REVERT: M 49 ASP cc_start: 0.7478 (m-30) cc_final: 0.7194 (m-30) REVERT: P 57 MET cc_start: 0.6824 (mmt) cc_final: 0.6428 (mtt) outliers start: 39 outliers final: 20 residues processed: 463 average time/residue: 0.2218 time to fit residues: 144.7393 Evaluate side-chains 422 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 401 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain P residue 15 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** B 31 ASN B 39 ASN C 39 ASN C 77 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 HIS H 85 ASN J 39 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 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: 0.7042 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11296 Z= 0.196 Angle : 0.611 10.097 15168 Z= 0.319 Chirality : 0.041 0.163 1712 Planarity : 0.004 0.036 1920 Dihedral : 5.023 22.920 1424 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.32 % Allowed : 15.59 % Favored : 81.09 % 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: -1.97 (0.22), residues: 1328 helix: -1.14 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.02 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP M 76 HIS 0.003 0.001 HIS D 56 PHE 0.028 0.002 PHE B 81 TYR 0.007 0.001 TYR F 78 ARG 0.007 0.001 ARG D 9 *********************** 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 488 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 446 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7935 (m-30) cc_final: 0.7731 (m-30) REVERT: B 64 GLU cc_start: 0.8084 (pp20) cc_final: 0.7768 (tm-30) REVERT: B 84 LEU cc_start: 0.8350 (tp) cc_final: 0.8124 (tp) REVERT: C 25 ASP cc_start: 0.7167 (t0) cc_final: 0.6932 (t0) REVERT: C 49 ASP cc_start: 0.7878 (t0) cc_final: 0.6965 (t0) REVERT: C 57 MET cc_start: 0.8259 (mtp) cc_final: 0.8021 (mtp) REVERT: E 1 MET cc_start: 0.6283 (tpp) cc_final: 0.6071 (tpp) REVERT: E 47 GLU cc_start: 0.7469 (pt0) cc_final: 0.7226 (pt0) REVERT: H 1 MET cc_start: 0.8215 (tpp) cc_final: 0.7692 (tpp) REVERT: H 55 ILE cc_start: 0.7662 (tt) cc_final: 0.7121 (mt) REVERT: J 26 ASP cc_start: 0.7638 (m-30) cc_final: 0.7251 (m-30) REVERT: K 22 GLN cc_start: 0.7981 (tp40) cc_final: 0.7669 (mm110) REVERT: K 27 LEU cc_start: 0.8841 (mm) cc_final: 0.8541 (mt) REVERT: L 36 GLU cc_start: 0.7623 (mm-30) cc_final: 0.6508 (mt-10) REVERT: M 20 ILE cc_start: 0.7607 (mm) cc_final: 0.7324 (mm) REVERT: N 26 ASP cc_start: 0.7787 (t0) cc_final: 0.7552 (t70) REVERT: N 57 MET cc_start: 0.6975 (mtm) cc_final: 0.6540 (mtm) REVERT: O 3 PHE cc_start: 0.7090 (t80) cc_final: 0.6838 (t80) REVERT: O 23 ILE cc_start: 0.8973 (mt) cc_final: 0.8712 (mt) REVERT: O 26 ASP cc_start: 0.7457 (m-30) cc_final: 0.7254 (m-30) REVERT: P 1 MET cc_start: 0.6932 (tpp) cc_final: 0.6512 (tpt) REVERT: P 57 MET cc_start: 0.7107 (mmt) cc_final: 0.6503 (mtt) outliers start: 42 outliers final: 29 residues processed: 463 average time/residue: 0.2174 time to fit residues: 142.4232 Evaluate side-chains 444 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 415 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 15 MET Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER 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: 0.8980 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 0.0170 chunk 55 optimal weight: 6.9990 chunk 78 optimal weight: 0.0670 chunk 116 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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** B 13 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN H 85 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.7931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11296 Z= 0.162 Angle : 0.556 10.078 15168 Z= 0.293 Chirality : 0.041 0.218 1712 Planarity : 0.003 0.036 1920 Dihedral : 4.640 23.031 1424 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.35 % Allowed : 17.41 % Favored : 78.24 % 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: -1.02 (0.23), residues: 1328 helix: -0.53 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -0.45 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP M 76 HIS 0.004 0.001 HIS M 56 PHE 0.028 0.001 PHE B 81 TYR 0.011 0.001 TYR O 78 ARG 0.005 0.000 ARG A 52 *********************** 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 504 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 449 time to evaluate : 1.391 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: A 80 LEU cc_start: 0.8480 (tp) cc_final: 0.8150 (tp) REVERT: C 17 MET cc_start: 0.8070 (tpt) cc_final: 0.7737 (tpt) REVERT: C 30 TRP cc_start: 0.8371 (m-10) cc_final: 0.8150 (m-10) REVERT: D 37 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6965 (mt-10) REVERT: E 1 MET cc_start: 0.6622 (tpp) cc_final: 0.5878 (tmm) REVERT: E 49 ASP cc_start: 0.7985 (m-30) cc_final: 0.7718 (m-30) REVERT: F 17 MET cc_start: 0.7867 (tpt) cc_final: 0.7571 (tpt) REVERT: F 49 ASP cc_start: 0.8532 (t0) cc_final: 0.8243 (t0) REVERT: G 39 ASN cc_start: 0.8768 (t0) cc_final: 0.8444 (t0) REVERT: H 1 MET cc_start: 0.8553 (tpp) cc_final: 0.8105 (tpp) REVERT: H 3 PHE cc_start: 0.8035 (t80) cc_final: 0.7749 (t80) REVERT: I 12 ILE cc_start: 0.9045 (pt) cc_final: 0.8730 (mt) REVERT: I 37 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7951 (mt-10) REVERT: J 1 MET cc_start: 0.7171 (tpp) cc_final: 0.6955 (tpp) REVERT: J 26 ASP cc_start: 0.7933 (m-30) cc_final: 0.7436 (m-30) REVERT: K 9 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7745 (mtt-85) REVERT: K 22 GLN cc_start: 0.8150 (tp40) cc_final: 0.7845 (mm110) REVERT: K 78 TYR cc_start: 0.7540 (t80) cc_final: 0.7311 (t80) REVERT: L 26 ASP cc_start: 0.7420 (m-30) cc_final: 0.6897 (m-30) REVERT: L 36 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6741 (mt-10) REVERT: L 76 TRP cc_start: 0.6080 (OUTLIER) cc_final: 0.5871 (m100) REVERT: M 20 ILE cc_start: 0.7846 (mm) cc_final: 0.7519 (mm) REVERT: O 23 ILE cc_start: 0.9141 (mt) cc_final: 0.8779 (mp) REVERT: P 57 MET cc_start: 0.7182 (mmt) cc_final: 0.6887 (mtt) REVERT: P 81 PHE cc_start: 0.8161 (t80) cc_final: 0.7951 (t80) outliers start: 55 outliers final: 27 residues processed: 473 average time/residue: 0.2256 time to fit residues: 151.4073 Evaluate side-chains 455 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 427 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 76 TRP Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.0904 ------------------------------------------------------------------------------- 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 77 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN F 77 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 GLN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.9781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11296 Z= 0.220 Angle : 0.599 9.691 15168 Z= 0.315 Chirality : 0.042 0.167 1712 Planarity : 0.003 0.036 1920 Dihedral : 4.583 24.240 1424 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.03 % Allowed : 19.22 % Favored : 76.74 % 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: -0.83 (0.23), residues: 1328 helix: -0.32 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 76 HIS 0.003 0.001 HIS M 56 PHE 0.034 0.002 PHE A 81 TYR 0.015 0.001 TYR A 78 ARG 0.006 0.001 ARG N 52 *********************** 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 545 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 494 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.7879 (mtt) cc_final: 0.7622 (mtp) REVERT: A 80 LEU cc_start: 0.8985 (tp) cc_final: 0.8716 (tp) REVERT: B 1 MET cc_start: 0.7106 (tpp) cc_final: 0.6795 (tpp) REVERT: B 82 GLN cc_start: 0.8100 (mm110) cc_final: 0.7873 (mm110) REVERT: C 21 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8501 (mtmt) REVERT: C 30 TRP cc_start: 0.8629 (m-10) cc_final: 0.7976 (m-10) REVERT: C 69 PHE cc_start: 0.8224 (t80) cc_final: 0.8008 (t80) REVERT: E 22 GLN cc_start: 0.8035 (mt0) cc_final: 0.7746 (mt0) REVERT: E 24 THR cc_start: 0.9056 (p) cc_final: 0.8827 (p) REVERT: E 47 GLU cc_start: 0.7628 (pt0) cc_final: 0.7227 (pt0) REVERT: E 84 LEU cc_start: 0.8407 (tp) cc_final: 0.7975 (tp) REVERT: F 27 LEU cc_start: 0.9312 (mm) cc_final: 0.8831 (mt) REVERT: F 49 ASP cc_start: 0.8515 (t0) cc_final: 0.8175 (t0) REVERT: G 18 THR cc_start: 0.8312 (p) cc_final: 0.7986 (p) REVERT: G 39 ASN cc_start: 0.8938 (t0) cc_final: 0.8685 (t0) REVERT: H 1 MET cc_start: 0.8617 (tpp) cc_final: 0.8317 (tpp) REVERT: H 3 PHE cc_start: 0.8461 (t80) cc_final: 0.8159 (t80) REVERT: H 45 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7966 (mtpp) REVERT: H 60 LYS cc_start: 0.8420 (mmtp) cc_final: 0.8110 (mmtm) REVERT: I 76 TRP cc_start: 0.7263 (m100) cc_final: 0.6918 (m100) REVERT: J 1 MET cc_start: 0.7371 (tpp) cc_final: 0.7067 (tpp) REVERT: J 26 ASP cc_start: 0.8422 (m-30) cc_final: 0.7954 (m-30) REVERT: J 63 SER cc_start: 0.8765 (p) cc_final: 0.8417 (t) REVERT: J 78 TYR cc_start: 0.8435 (t80) cc_final: 0.8217 (t80) REVERT: K 9 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7961 (mtt-85) REVERT: K 35 ARG cc_start: 0.7327 (mmm160) cc_final: 0.6973 (mmm160) REVERT: K 78 TYR cc_start: 0.7955 (t80) cc_final: 0.7569 (t80) REVERT: L 35 ARG cc_start: 0.8157 (tpt170) cc_final: 0.7882 (tpm170) REVERT: L 36 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7040 (mt-10) REVERT: M 1 MET cc_start: 0.8068 (tpp) cc_final: 0.7504 (tpp) REVERT: M 2 ASN cc_start: 0.8081 (t0) cc_final: 0.7735 (t0) REVERT: N 34 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8445 (p0) REVERT: N 55 ILE cc_start: 0.9239 (mm) cc_final: 0.9026 (mm) REVERT: N 59 LEU cc_start: 0.9243 (mt) cc_final: 0.8972 (mt) REVERT: O 44 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6471 (mt-10) REVERT: P 2 ASN cc_start: 0.8335 (m-40) cc_final: 0.8080 (m-40) REVERT: P 11 LEU cc_start: 0.9127 (mt) cc_final: 0.8926 (mt) outliers start: 51 outliers final: 26 residues processed: 515 average time/residue: 0.2322 time to fit residues: 167.7422 Evaluate side-chains 480 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 453 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 15 MET Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0826 > 50: distance: 60 - 64: 14.782 distance: 64 - 65: 6.761 distance: 65 - 66: 16.694 distance: 65 - 68: 25.613 distance: 66 - 67: 17.608 distance: 66 - 73: 9.526 distance: 68 - 69: 22.809 distance: 69 - 70: 21.884 distance: 70 - 71: 29.935 distance: 71 - 72: 55.945 distance: 73 - 74: 6.900 distance: 74 - 75: 4.786 distance: 74 - 77: 13.645 distance: 75 - 76: 27.392 distance: 75 - 82: 26.224 distance: 77 - 78: 7.296 distance: 78 - 79: 9.668 distance: 79 - 80: 17.904 distance: 80 - 81: 38.113 distance: 82 - 83: 7.344 distance: 83 - 84: 24.571 distance: 84 - 85: 16.972 distance: 84 - 86: 16.083 distance: 86 - 87: 3.885 distance: 87 - 88: 6.751 distance: 87 - 90: 11.463 distance: 88 - 89: 14.635 distance: 88 - 92: 15.868 distance: 90 - 91: 13.079 distance: 92 - 93: 5.458 distance: 93 - 96: 5.643 distance: 94 - 95: 11.351 distance: 94 - 101: 8.117 distance: 96 - 97: 8.431 distance: 97 - 98: 3.408 distance: 98 - 99: 3.631 distance: 98 - 100: 5.592 distance: 101 - 102: 6.638 distance: 102 - 103: 10.539 distance: 102 - 105: 10.233 distance: 103 - 104: 21.717 distance: 103 - 107: 20.958 distance: 105 - 106: 7.541 distance: 107 - 108: 17.469 distance: 108 - 111: 16.056 distance: 109 - 110: 19.624 distance: 109 - 113: 25.196 distance: 110 - 140: 32.603 distance: 111 - 112: 6.695 distance: 113 - 114: 11.092 distance: 114 - 115: 14.894 distance: 114 - 117: 5.754 distance: 115 - 116: 8.440 distance: 115 - 121: 10.607 distance: 116 - 147: 11.981 distance: 117 - 118: 6.749 distance: 118 - 119: 5.632 distance: 118 - 120: 10.612 distance: 121 - 122: 12.546 distance: 122 - 123: 13.975 distance: 122 - 125: 6.864 distance: 123 - 124: 5.562 distance: 123 - 129: 9.649 distance: 124 - 156: 21.757 distance: 125 - 126: 10.590 distance: 126 - 127: 10.551 distance: 126 - 128: 21.190 distance: 129 - 130: 9.497 distance: 130 - 131: 6.022 distance: 130 - 133: 18.085 distance: 131 - 132: 9.858 distance: 131 - 140: 16.940 distance: 132 - 162: 25.757 distance: 133 - 134: 7.163 distance: 134 - 135: 10.413 distance: 134 - 136: 4.161 distance: 135 - 137: 7.458 distance: 136 - 138: 8.718 distance: 137 - 139: 12.952 distance: 138 - 139: 5.130