Starting phenix.real_space_refine (version: dev) on Sun Feb 26 01:12:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/02_2023/7pzd_13727_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/02_2023/7pzd_13727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/02_2023/7pzd_13727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/02_2023/7pzd_13727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/02_2023/7pzd_13727_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/02_2023/7pzd_13727_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13338 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "G ARG 7": "NH1" <-> "NH2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "I ARG 7": "NH1" <-> "NH2" Residue "I ARG 43": "NH1" <-> "NH2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I GLU 65": "OE1" <-> "OE2" Residue "J ARG 7": "NH1" <-> "NH2" Residue "J ARG 43": "NH1" <-> "NH2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "K ARG 7": "NH1" <-> "NH2" Residue "K ARG 43": "NH1" <-> "NH2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 43": "NH1" <-> "NH2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "M ARG 7": "NH1" <-> "NH2" Residue "M ARG 43": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "N ARG 7": "NH1" <-> "NH2" Residue "N ARG 43": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N GLU 65": "OE1" <-> "OE2" Residue "O ARG 7": "NH1" <-> "NH2" Residue "O ARG 43": "NH1" <-> "NH2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O GLU 65": "OE1" <-> "OE2" Residue "P ARG 7": "NH1" <-> "NH2" Residue "P ARG 43": "NH1" <-> "NH2" Residue "P GLU 47": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "Q ARG 7": "NH1" <-> "NH2" Residue "Q ARG 43": "NH1" <-> "NH2" Residue "Q GLU 47": "OE1" <-> "OE2" Residue "Q GLU 65": "OE1" <-> "OE2" Residue "R ARG 7": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "S ARG 7": "NH1" <-> "NH2" Residue "S ARG 43": "NH1" <-> "NH2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "T ARG 7": "NH1" <-> "NH2" Residue "T ARG 43": "NH1" <-> "NH2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T GLU 65": "OE1" <-> "OE2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U ARG 43": "NH1" <-> "NH2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U GLU 65": "OE1" <-> "OE2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V ARG 43": "NH1" <-> "NH2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V GLU 65": "OE1" <-> "OE2" Residue "W ARG 7": "NH1" <-> "NH2" Residue "W ARG 43": "NH1" <-> "NH2" Residue "W GLU 47": "OE1" <-> "OE2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "X ARG 7": "NH1" <-> "NH2" Residue "X ARG 43": "NH1" <-> "NH2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13644 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "H" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "I" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "J" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "K" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "M" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "N" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "O" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "P" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "Q" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "R" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "S" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "T" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "U" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "V" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "W" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "X" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Time building chain proxies: 7.58, per 1000 atoms: 0.56 Number of scatterers: 13644 At special positions: 0 Unit cell: (96.03, 99.231, 110.968, 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 108 16.00 O 2466 8.00 N 2358 7.00 C 8712 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: 5.44 Conformation dependent library (CDL) restraints added in 2.0 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'G' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS G 23 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 49 Processing helix chain 'G' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N GLU G 65 " --> pdb=" O PHE G 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS G 66 " --> pdb=" O ASN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'H' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS H 23 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP H 31 " --> pdb=" O MET H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 49 Processing helix chain 'H' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N GLU H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 90 Processing helix chain 'I' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP I 31 " --> pdb=" O MET I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 49 Processing helix chain 'I' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP I 60 " --> pdb=" O THR I 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU I 65 " --> pdb=" O PHE I 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 90 Processing helix chain 'J' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP J 31 " --> pdb=" O MET J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 49 Processing helix chain 'J' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE J 59 " --> pdb=" O ALA J 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS J 66 " --> pdb=" O ASN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 Processing helix chain 'K' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS K 23 " --> pdb=" O ASP K 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP K 31 " --> pdb=" O MET K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 49 Processing helix chain 'K' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU K 65 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS K 66 " --> pdb=" O ASN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 Processing helix chain 'L' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS L 23 " --> pdb=" O ASP L 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP L 31 " --> pdb=" O MET L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 49 Processing helix chain 'L' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE L 59 " --> pdb=" O ALA L 55 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP L 60 " --> pdb=" O THR L 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 9.873A pdb=" N GLU L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS L 66 " --> pdb=" O ASN L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 90 Processing helix chain 'M' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS M 9 " --> pdb=" O SER M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 31 removed outlier: 3.546A pdb=" N LYS M 23 " --> pdb=" O ASP M 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP M 31 " --> pdb=" O MET M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 49 Processing helix chain 'M' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP M 60 " --> pdb=" O THR M 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU M 65 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS M 66 " --> pdb=" O ASN M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 90 Processing helix chain 'N' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS N 9 " --> pdb=" O SER N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS N 23 " --> pdb=" O ASP N 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP N 31 " --> pdb=" O MET N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 49 Processing helix chain 'N' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP N 60 " --> pdb=" O THR N 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU N 65 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS N 66 " --> pdb=" O ASN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 Processing helix chain 'O' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP O 31 " --> pdb=" O MET O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 49 Processing helix chain 'O' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU O 65 " --> pdb=" O PHE O 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS O 66 " --> pdb=" O ASN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 Processing helix chain 'P' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS P 9 " --> pdb=" O SER P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS P 23 " --> pdb=" O ASP P 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP P 31 " --> pdb=" O MET P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 49 Processing helix chain 'P' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP P 60 " --> pdb=" O THR P 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU P 64 " --> pdb=" O ASP P 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU P 65 " --> pdb=" O PHE P 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS P 66 " --> pdb=" O ASN P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 90 Processing helix chain 'Q' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS Q 9 " --> pdb=" O SER Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS Q 23 " --> pdb=" O ASP Q 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP Q 31 " --> pdb=" O MET Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 49 Processing helix chain 'Q' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU Q 64 " --> pdb=" O ASP Q 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS Q 66 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 90 Processing helix chain 'R' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS R 9 " --> pdb=" O SER R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS R 23 " --> pdb=" O ASP R 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP R 31 " --> pdb=" O MET R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 49 Processing helix chain 'R' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP R 60 " --> pdb=" O THR R 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU R 64 " --> pdb=" O ASP R 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU R 65 " --> pdb=" O PHE R 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 90 Processing helix chain 'S' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS S 9 " --> pdb=" O SER S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS S 23 " --> pdb=" O ASP S 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP S 31 " --> pdb=" O MET S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 49 Processing helix chain 'S' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE S 59 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP S 60 " --> pdb=" O THR S 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU S 64 " --> pdb=" O ASP S 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU S 65 " --> pdb=" O PHE S 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS S 66 " --> pdb=" O ASN S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 90 Processing helix chain 'T' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS T 9 " --> pdb=" O SER T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 31 removed outlier: 3.546A pdb=" N LYS T 23 " --> pdb=" O ASP T 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP T 31 " --> pdb=" O MET T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 49 Processing helix chain 'T' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE T 59 " --> pdb=" O ALA T 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP T 60 " --> pdb=" O THR T 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU T 64 " --> pdb=" O ASP T 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU T 65 " --> pdb=" O PHE T 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS T 66 " --> pdb=" O ASN T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 90 Processing helix chain 'U' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS U 9 " --> pdb=" O SER U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS U 23 " --> pdb=" O ASP U 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 49 Processing helix chain 'U' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE U 59 " --> pdb=" O ALA U 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP U 60 " --> pdb=" O THR U 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU U 65 " --> pdb=" O PHE U 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS U 66 " --> pdb=" O ASN U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 90 Processing helix chain 'V' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS V 9 " --> pdb=" O SER V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 31 removed outlier: 3.544A pdb=" N LYS V 23 " --> pdb=" O ASP V 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP V 31 " --> pdb=" O MET V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE V 59 " --> pdb=" O ALA V 55 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP V 60 " --> pdb=" O THR V 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU V 64 " --> pdb=" O ASP V 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU V 65 " --> pdb=" O PHE V 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS V 66 " --> pdb=" O ASN V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 80 through 90 Processing helix chain 'W' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS W 9 " --> pdb=" O SER W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS W 23 " --> pdb=" O ASP W 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP W 31 " --> pdb=" O MET W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 49 Processing helix chain 'W' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP W 60 " --> pdb=" O THR W 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU W 64 " --> pdb=" O ASP W 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU W 65 " --> pdb=" O PHE W 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 90 Processing helix chain 'X' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS X 9 " --> pdb=" O SER X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP X 31 " --> pdb=" O MET X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 49 Processing helix chain 'X' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE X 59 " --> pdb=" O ALA X 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP X 60 " --> pdb=" O THR X 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU X 64 " --> pdb=" O ASP X 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU X 65 " --> pdb=" O PHE X 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS X 66 " --> pdb=" O ASN X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 80 through 90 756 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 5.84 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: 4396 1.34 - 1.46: 2050 1.46 - 1.58: 7342 1.58 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 13968 Sorted by residual: bond pdb=" N VAL K 52 " pdb=" CA VAL K 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 bond pdb=" N VAL W 52 " pdb=" CA VAL W 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 bond pdb=" N VAL G 52 " pdb=" CA VAL G 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 bond pdb=" N VAL H 52 " pdb=" CA VAL H 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 bond pdb=" N VAL Q 52 " pdb=" CA VAL Q 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 ... (remaining 13963 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.02: 522 107.02 - 113.79: 7740 113.79 - 120.56: 5918 120.56 - 127.33: 4416 127.33 - 134.10: 214 Bond angle restraints: 18810 Sorted by residual: angle pdb=" N ASP L 53 " pdb=" CA ASP L 53 " pdb=" C ASP L 53 " ideal model delta sigma weight residual 113.38 106.17 7.21 1.23e+00 6.61e-01 3.43e+01 angle pdb=" N ASP G 53 " pdb=" CA ASP G 53 " pdb=" C ASP G 53 " ideal model delta sigma weight residual 113.38 106.19 7.19 1.23e+00 6.61e-01 3.42e+01 angle pdb=" N ASP T 53 " pdb=" CA ASP T 53 " pdb=" C ASP T 53 " ideal model delta sigma weight residual 113.38 106.19 7.19 1.23e+00 6.61e-01 3.41e+01 angle pdb=" N ASP Q 53 " pdb=" CA ASP Q 53 " pdb=" C ASP Q 53 " ideal model delta sigma weight residual 113.38 106.19 7.19 1.23e+00 6.61e-01 3.41e+01 angle pdb=" N ASP V 53 " pdb=" CA ASP V 53 " pdb=" C ASP V 53 " ideal model delta sigma weight residual 113.38 106.19 7.19 1.23e+00 6.61e-01 3.41e+01 ... (remaining 18805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.38: 7254 15.38 - 30.77: 954 30.77 - 46.15: 216 46.15 - 61.54: 144 61.54 - 76.92: 36 Dihedral angle restraints: 8604 sinusoidal: 3708 harmonic: 4896 Sorted by residual: dihedral pdb=" CA PRO S 33 " pdb=" C PRO S 33 " pdb=" N PRO S 34 " pdb=" CA PRO S 34 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PRO M 33 " pdb=" C PRO M 33 " pdb=" N PRO M 34 " pdb=" CA PRO M 34 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PRO H 33 " pdb=" C PRO H 33 " pdb=" N PRO H 34 " pdb=" CA PRO H 34 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 8601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 954 0.042 - 0.084: 482 0.084 - 0.126: 292 0.126 - 0.167: 162 0.167 - 0.209: 54 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CA ASP N 53 " pdb=" N ASP N 53 " pdb=" C ASP N 53 " pdb=" CB ASP N 53 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASP R 53 " pdb=" N ASP R 53 " pdb=" C ASP R 53 " pdb=" CB ASP R 53 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASP V 53 " pdb=" N ASP V 53 " pdb=" C ASP V 53 " pdb=" CB ASP V 53 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1941 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA P 49 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.31e+00 pdb=" C ALA P 49 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA P 49 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP P 50 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA S 49 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ALA S 49 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA S 49 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP S 50 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA V 49 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ALA V 49 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA V 49 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP V 50 " -0.013 2.00e-02 2.50e+03 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5346 2.89 - 3.39: 12700 3.39 - 3.89: 21161 3.89 - 4.40: 24040 4.40 - 4.90: 41222 Nonbonded interactions: 104469 Sorted by model distance: nonbonded pdb=" OD1 ASP G 82 " pdb=" N LEU G 83 " model vdw 2.384 2.520 nonbonded pdb=" OD1 ASP N 82 " pdb=" N LEU N 83 " model vdw 2.384 2.520 nonbonded pdb=" OD1 ASP U 82 " pdb=" N LEU U 83 " model vdw 2.384 2.520 nonbonded pdb=" OD1 ASP P 82 " pdb=" N LEU P 83 " model vdw 2.384 2.520 nonbonded pdb=" OD1 ASP Q 82 " pdb=" N LEU Q 83 " model vdw 2.384 2.520 ... (remaining 104464 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 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 8712 2.51 5 N 2358 2.21 5 O 2466 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 3.420 Check model and map are aligned: 0.190 Process input model: 34.630 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.010 0.037 13968 Z= 0.631 Angle : 1.241 7.207 18810 Z= 0.880 Chirality : 0.075 0.209 1944 Planarity : 0.007 0.032 2412 Dihedral : 16.787 76.919 5400 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 1.27 % 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: -3.73 (0.16), residues: 1620 helix: -2.31 (0.11), residues: 1296 sheet: None (None), residues: 0 loop : -2.09 (0.23), residues: 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 549 time to evaluate : 1.739 Fit side-chains outliers start: 18 outliers final: 4 residues processed: 567 average time/residue: 0.3525 time to fit residues: 262.7496 Evaluate side-chains 461 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 457 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6622 time to fit residues: 5.4722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 45 GLN G 62 ASN ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN J 28 HIS J 45 GLN J 51 HIS K 28 HIS K 45 GLN L 28 HIS L 45 GLN M 28 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 ASN N 28 HIS N 45 GLN N 62 ASN O 28 HIS ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN P 28 HIS P 45 GLN P 62 ASN Q 28 HIS Q 62 ASN R 28 HIS R 45 GLN S 28 HIS S 45 GLN S 51 HIS S 62 ASN S 79 ASN T 28 HIS T 45 GLN T 62 ASN U 28 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN V 28 HIS V 51 HIS V 62 ASN W 28 HIS W 51 HIS W 62 ASN X 28 HIS X 62 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13968 Z= 0.230 Angle : 0.620 6.631 18810 Z= 0.340 Chirality : 0.038 0.154 1944 Planarity : 0.005 0.037 2412 Dihedral : 4.324 15.474 1800 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 3.52 % 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: -0.55 (0.21), residues: 1620 helix: -0.22 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.29 (0.38), residues: 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 466 time to evaluate : 1.768 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 29 residues processed: 487 average time/residue: 0.3280 time to fit residues: 214.5183 Evaluate side-chains 465 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 436 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2055 time to fit residues: 11.7478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 13968 Z= 0.222 Angle : 0.565 5.978 18810 Z= 0.304 Chirality : 0.036 0.145 1944 Planarity : 0.005 0.041 2412 Dihedral : 4.179 15.527 1800 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.04 % 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: 0.08 (0.21), residues: 1620 helix: 0.31 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.50 (0.37), residues: 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 449 time to evaluate : 1.647 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 459 average time/residue: 0.3413 time to fit residues: 209.3885 Evaluate side-chains 443 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 428 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1762 time to fit residues: 6.2944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13968 Z= 0.207 Angle : 0.542 5.428 18810 Z= 0.292 Chirality : 0.035 0.147 1944 Planarity : 0.005 0.046 2412 Dihedral : 4.062 15.867 1800 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.13 % 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: 0.33 (0.20), residues: 1620 helix: 0.58 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.89 (0.35), residues: 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 443 time to evaluate : 1.514 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 450 average time/residue: 0.3286 time to fit residues: 198.5793 Evaluate side-chains 436 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 426 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1356 time to fit residues: 4.6952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13968 Z= 0.279 Angle : 0.573 5.572 18810 Z= 0.308 Chirality : 0.037 0.139 1944 Planarity : 0.005 0.046 2412 Dihedral : 4.188 16.217 1800 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1620 helix: 0.67 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.21 (0.33), residues: 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 438 time to evaluate : 1.698 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 444 average time/residue: 0.3338 time to fit residues: 198.3401 Evaluate side-chains 441 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 426 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1805 time to fit residues: 6.7319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13968 Z= 0.230 Angle : 0.550 5.814 18810 Z= 0.297 Chirality : 0.035 0.143 1944 Planarity : 0.005 0.051 2412 Dihedral : 4.123 16.226 1800 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.27 % 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: 0.57 (0.20), residues: 1620 helix: 0.86 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.33 (0.32), residues: 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 439 time to evaluate : 1.777 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 444 average time/residue: 0.3373 time to fit residues: 200.2575 Evaluate side-chains 440 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 427 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1847 time to fit residues: 6.2498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 114 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13968 Z= 0.259 Angle : 0.570 5.929 18810 Z= 0.308 Chirality : 0.036 0.142 1944 Planarity : 0.006 0.053 2412 Dihedral : 4.164 16.279 1800 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.84 % 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: 0.63 (0.20), residues: 1620 helix: 0.94 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.51 (0.32), residues: 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 438 time to evaluate : 1.705 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 442 average time/residue: 0.3360 time to fit residues: 198.8876 Evaluate side-chains 431 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 427 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1507 time to fit residues: 3.3448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 122 optimal weight: 0.2980 chunk 142 optimal weight: 6.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 13968 Z= 0.253 Angle : 0.581 6.818 18810 Z= 0.315 Chirality : 0.036 0.164 1944 Planarity : 0.006 0.060 2412 Dihedral : 4.174 16.328 1800 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1620 helix: 0.89 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.20 (0.33), residues: 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 437 time to evaluate : 1.626 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 440 average time/residue: 0.3363 time to fit residues: 197.5930 Evaluate side-chains 432 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 427 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1779 time to fit residues: 3.4930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.0270 chunk 136 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 13968 Z= 0.237 Angle : 0.592 7.694 18810 Z= 0.321 Chirality : 0.036 0.149 1944 Planarity : 0.006 0.061 2412 Dihedral : 4.116 16.292 1800 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.35 % 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: 0.75 (0.20), residues: 1620 helix: 0.94 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.18 (0.33), residues: 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 420 time to evaluate : 1.605 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 420 average time/residue: 0.3393 time to fit residues: 190.5284 Evaluate side-chains 418 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 414 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1418 time to fit residues: 3.3236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 106 optimal weight: 0.0980 chunk 161 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 overall best weight: 1.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13968 Z= 0.239 Angle : 0.593 8.675 18810 Z= 0.323 Chirality : 0.036 0.155 1944 Planarity : 0.006 0.062 2412 Dihedral : 4.107 16.283 1800 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.28 % 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: 0.76 (0.20), residues: 1620 helix: 0.95 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 1.830 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 421 average time/residue: 0.3373 time to fit residues: 190.1659 Evaluate side-chains 418 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 414 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1600 time to fit residues: 3.2537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 0.0070 chunk 118 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 0.0050 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.149125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130859 restraints weight = 17383.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.135133 restraints weight = 9877.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137965 restraints weight = 6439.282| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13968 Z= 0.186 Angle : 0.574 7.345 18810 Z= 0.313 Chirality : 0.034 0.148 1944 Planarity : 0.006 0.059 2412 Dihedral : 3.844 15.893 1800 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.28 % 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: 1.01 (0.21), residues: 1620 helix: 1.16 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.13 (0.34), residues: 324 =============================================================================== Job complete usr+sys time: 3447.67 seconds wall clock time: 63 minutes 8.06 seconds (3788.06 seconds total)