Starting phenix.real_space_refine on Wed Mar 20 09:11:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/03_2024/7pzd_13727_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/03_2024/7pzd_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_13727/03_2024/7pzd_13727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/03_2024/7pzd_13727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/03_2024/7pzd_13727_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/03_2024/7pzd_13727_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.08, per 1000 atoms: 0.52 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: 4.88 Conformation dependent library (CDL) restraints added in 2.2 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: 1.10 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: 3.14 Time building geometry restraints manager: 5.35 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 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 2.950 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.450 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 % Allowed : 13.92 % Favored : 84.81 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 94 HIS 0.005 0.002 HIS G 28 PHE 0.019 0.004 PHE G 75 TYR 0.008 0.003 TYR W 13 ARG 0.014 0.001 ARG U 81 *********************** 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 : 1.621 Fit side-chains REVERT: G 43 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7561 (mtp-110) REVERT: G 81 ARG cc_start: 0.7615 (mmt180) cc_final: 0.6678 (ptt180) REVERT: H 43 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7617 (mtp-110) REVERT: H 81 ARG cc_start: 0.7385 (mmt180) cc_final: 0.6374 (ptt180) REVERT: I 81 ARG cc_start: 0.7816 (mmt180) cc_final: 0.6818 (ptt180) REVERT: J 62 ASN cc_start: 0.9029 (m-40) cc_final: 0.8569 (m-40) REVERT: J 81 ARG cc_start: 0.7781 (mmt180) cc_final: 0.6978 (mtp180) REVERT: K 62 ASN cc_start: 0.8968 (m-40) cc_final: 0.8664 (m-40) REVERT: K 89 ARG cc_start: 0.8573 (mtm110) cc_final: 0.8356 (mtm110) REVERT: L 62 ASN cc_start: 0.9027 (m-40) cc_final: 0.8601 (m-40) REVERT: L 81 ARG cc_start: 0.8086 (mmt180) cc_final: 0.7412 (mtm180) REVERT: L 90 ASP cc_start: 0.7451 (t0) cc_final: 0.7234 (t0) REVERT: N 90 ASP cc_start: 0.7613 (t0) cc_final: 0.7291 (t0) REVERT: O 43 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7594 (mtp180) REVERT: O 90 ASP cc_start: 0.7692 (t0) cc_final: 0.7492 (t0) REVERT: P 31 ASP cc_start: 0.8417 (m-30) cc_final: 0.8166 (m-30) REVERT: P 70 MET cc_start: 0.8179 (mtp) cc_final: 0.7938 (mtp) REVERT: Q 30 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7834 (mt-10) REVERT: Q 62 ASN cc_start: 0.8840 (m-40) cc_final: 0.8470 (m110) REVERT: Q 90 ASP cc_start: 0.7994 (t0) cc_final: 0.7655 (t0) REVERT: R 62 ASN cc_start: 0.8919 (m-40) cc_final: 0.8314 (m-40) REVERT: S 30 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7181 (mt-10) REVERT: S 43 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7179 (mtp180) REVERT: T 30 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7411 (mt-10) REVERT: T 43 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7149 (mtp180) REVERT: T 70 MET cc_start: 0.8088 (mtp) cc_final: 0.7757 (mtp) REVERT: U 16 ASP cc_start: 0.8091 (t0) cc_final: 0.7866 (t0) REVERT: U 30 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7419 (mt-10) REVERT: U 43 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7058 (mtp180) REVERT: U 62 ASN cc_start: 0.8991 (m-40) cc_final: 0.8578 (m110) REVERT: V 31 ASP cc_start: 0.8197 (m-30) cc_final: 0.7983 (m-30) REVERT: V 62 ASN cc_start: 0.9131 (m-40) cc_final: 0.8925 (m110) REVERT: X 91 GLU cc_start: 0.7788 (tt0) cc_final: 0.7586 (tt0) outliers start: 18 outliers final: 4 residues processed: 567 average time/residue: 0.3404 time to fit residues: 253.5183 Evaluate side-chains 473 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 463 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain H residue 43 ARG Chi-restraints excluded: chain J residue 43 ARG Chi-restraints excluded: chain K residue 43 ARG Chi-restraints excluded: chain L residue 43 ARG Chi-restraints excluded: chain N residue 43 ARG Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 43 ARG Chi-restraints excluded: chain T residue 43 ARG Chi-restraints excluded: chain U residue 43 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 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** V 28 HIS V 51 HIS W 28 HIS W 51 HIS W 62 ASN X 28 HIS X 62 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2859 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= 0.214 Angle : 0.612 5.806 18810 Z= 0.335 Chirality : 0.038 0.152 1944 Planarity : 0.005 0.037 2412 Dihedral : 5.011 29.920 1840 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 3.59 % Allowed : 19.06 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1620 helix: -0.17 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 73 HIS 0.008 0.003 HIS L 51 PHE 0.013 0.002 PHE J 25 TYR 0.022 0.002 TYR Q 32 ARG 0.008 0.001 ARG H 89 *********************** 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 523 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 472 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7413 (mmt180) cc_final: 0.6987 (ptt180) REVERT: G 90 ASP cc_start: 0.7503 (m-30) cc_final: 0.7299 (t0) REVERT: H 18 GLU cc_start: 0.7603 (pm20) cc_final: 0.7273 (pm20) REVERT: I 81 ARG cc_start: 0.7255 (mmt180) cc_final: 0.6602 (ptt180) REVERT: I 90 ASP cc_start: 0.7114 (t0) cc_final: 0.6870 (t0) REVERT: J 31 ASP cc_start: 0.8114 (m-30) cc_final: 0.7678 (m-30) REVERT: J 62 ASN cc_start: 0.8871 (m-40) cc_final: 0.8395 (m-40) REVERT: J 89 ARG cc_start: 0.8305 (mtm110) cc_final: 0.7855 (mtm110) REVERT: K 13 TYR cc_start: 0.8253 (m-10) cc_final: 0.8026 (m-10) REVERT: K 31 ASP cc_start: 0.8268 (m-30) cc_final: 0.8047 (m-30) REVERT: K 62 ASN cc_start: 0.8843 (m-40) cc_final: 0.8504 (m110) REVERT: K 90 ASP cc_start: 0.7150 (t0) cc_final: 0.6864 (t0) REVERT: L 13 TYR cc_start: 0.8350 (m-10) cc_final: 0.7939 (m-10) REVERT: L 56 THR cc_start: 0.8646 (t) cc_final: 0.8390 (m) REVERT: L 62 ASN cc_start: 0.8868 (m-40) cc_final: 0.8413 (m-40) REVERT: L 70 MET cc_start: 0.8163 (mtm) cc_final: 0.7959 (mtm) REVERT: L 81 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7063 (mtm110) REVERT: L 90 ASP cc_start: 0.7560 (t0) cc_final: 0.7210 (t0) REVERT: N 31 ASP cc_start: 0.8341 (m-30) cc_final: 0.7956 (m-30) REVERT: N 90 ASP cc_start: 0.7601 (t0) cc_final: 0.7289 (t0) REVERT: O 16 ASP cc_start: 0.8795 (t0) cc_final: 0.8593 (t0) REVERT: O 90 ASP cc_start: 0.7818 (t0) cc_final: 0.7384 (t0) REVERT: P 27 MET cc_start: 0.8437 (ttt) cc_final: 0.8073 (ttt) REVERT: P 90 ASP cc_start: 0.7692 (t0) cc_final: 0.7237 (t0) REVERT: Q 31 ASP cc_start: 0.8230 (m-30) cc_final: 0.8017 (m-30) REVERT: Q 62 ASN cc_start: 0.8616 (m-40) cc_final: 0.8283 (m-40) REVERT: Q 90 ASP cc_start: 0.7924 (t0) cc_final: 0.7409 (t0) REVERT: R 62 ASN cc_start: 0.8608 (m-40) cc_final: 0.7957 (m-40) REVERT: R 90 ASP cc_start: 0.7687 (t0) cc_final: 0.7352 (t0) REVERT: S 47 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6865 (mm-30) REVERT: T 30 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7211 (mt-10) REVERT: T 90 ASP cc_start: 0.8056 (t0) cc_final: 0.7790 (t0) REVERT: U 30 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7121 (mt-10) REVERT: U 31 ASP cc_start: 0.7999 (m-30) cc_final: 0.7766 (m-30) REVERT: U 47 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6607 (mm-30) REVERT: U 62 ASN cc_start: 0.8894 (m-40) cc_final: 0.8406 (m110) REVERT: U 90 ASP cc_start: 0.7783 (t0) cc_final: 0.7563 (t0) REVERT: V 36 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7165 (mtpp) REVERT: V 62 ASN cc_start: 0.9003 (m-40) cc_final: 0.8695 (m-40) REVERT: V 85 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7331 (mt-10) REVERT: W 16 ASP cc_start: 0.8469 (t0) cc_final: 0.8020 (t0) REVERT: W 31 ASP cc_start: 0.7956 (m-30) cc_final: 0.7685 (m-30) REVERT: W 90 ASP cc_start: 0.7749 (t0) cc_final: 0.7470 (t0) REVERT: X 36 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6959 (mtpt) outliers start: 51 outliers final: 29 residues processed: 493 average time/residue: 0.3125 time to fit residues: 208.3329 Evaluate side-chains 476 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 445 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 51 HIS Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 51 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 27 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain S residue 51 HIS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain V residue 36 LYS Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 51 HIS Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 88 LYS 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: 0.7980 chunk 147 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** X 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13968 Z= 0.207 Angle : 0.556 5.674 18810 Z= 0.300 Chirality : 0.036 0.137 1944 Planarity : 0.005 0.041 2412 Dihedral : 4.182 15.203 1800 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.53 % Allowed : 21.03 % Favored : 76.44 % 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: 0.18 (0.21), residues: 1620 helix: 0.35 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.32 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP U 68 HIS 0.009 0.002 HIS H 51 PHE 0.014 0.002 PHE G 25 TYR 0.023 0.002 TYR J 84 ARG 0.009 0.000 ARG K 89 *********************** 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 488 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 452 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7521 (mmt180) cc_final: 0.6997 (ptt180) REVERT: I 81 ARG cc_start: 0.7313 (mmt180) cc_final: 0.6634 (ptt180) REVERT: I 90 ASP cc_start: 0.7356 (t0) cc_final: 0.7022 (t0) REVERT: J 31 ASP cc_start: 0.8141 (m-30) cc_final: 0.7747 (m-30) REVERT: J 62 ASN cc_start: 0.8872 (m-40) cc_final: 0.8396 (m110) REVERT: K 13 TYR cc_start: 0.8289 (m-10) cc_final: 0.7879 (m-10) REVERT: K 62 ASN cc_start: 0.8848 (m-40) cc_final: 0.8437 (m-40) REVERT: K 90 ASP cc_start: 0.7243 (t0) cc_final: 0.6938 (t0) REVERT: L 13 TYR cc_start: 0.8347 (m-10) cc_final: 0.7971 (m-10) REVERT: L 56 THR cc_start: 0.8893 (t) cc_final: 0.8600 (m) REVERT: L 62 ASN cc_start: 0.8823 (m-40) cc_final: 0.8440 (m-40) REVERT: M 90 ASP cc_start: 0.7491 (t0) cc_final: 0.7262 (t0) REVERT: N 31 ASP cc_start: 0.8239 (m-30) cc_final: 0.7894 (m-30) REVERT: N 90 ASP cc_start: 0.7662 (t0) cc_final: 0.7228 (t0) REVERT: O 16 ASP cc_start: 0.8828 (t0) cc_final: 0.8494 (t0) REVERT: O 90 ASP cc_start: 0.7800 (t0) cc_final: 0.7343 (t0) REVERT: P 27 MET cc_start: 0.8454 (ttp) cc_final: 0.8092 (ttt) REVERT: P 31 ASP cc_start: 0.8394 (m-30) cc_final: 0.8131 (m-30) REVERT: P 90 ASP cc_start: 0.7670 (t0) cc_final: 0.7299 (t0) REVERT: Q 62 ASN cc_start: 0.8629 (m-40) cc_final: 0.8329 (m110) REVERT: Q 90 ASP cc_start: 0.7934 (t0) cc_final: 0.7415 (t0) REVERT: R 62 ASN cc_start: 0.8632 (m-40) cc_final: 0.7947 (m110) REVERT: R 90 ASP cc_start: 0.7572 (t0) cc_final: 0.7252 (t0) REVERT: S 27 MET cc_start: 0.8634 (ttp) cc_final: 0.8396 (ttt) REVERT: T 90 ASP cc_start: 0.8069 (t0) cc_final: 0.7838 (t0) REVERT: U 31 ASP cc_start: 0.8019 (m-30) cc_final: 0.7747 (m-30) REVERT: U 62 ASN cc_start: 0.8991 (m-40) cc_final: 0.8483 (m-40) REVERT: V 36 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7271 (mtpp) REVERT: V 62 ASN cc_start: 0.9061 (m-40) cc_final: 0.8691 (m-40) REVERT: V 85 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7401 (mt-10) REVERT: V 90 ASP cc_start: 0.7965 (t0) cc_final: 0.7757 (t0) REVERT: W 16 ASP cc_start: 0.8432 (t70) cc_final: 0.8052 (t0) REVERT: W 36 LYS cc_start: 0.7548 (mtpt) cc_final: 0.6979 (mtpp) REVERT: W 90 ASP cc_start: 0.7862 (t0) cc_final: 0.7621 (t0) REVERT: X 36 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7040 (mtpt) outliers start: 36 outliers final: 24 residues processed: 462 average time/residue: 0.3160 time to fit residues: 196.1373 Evaluate side-chains 460 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 434 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 51 HIS Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 27 MET Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 36 LYS Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 88 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 51 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3650 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= 0.200 Angle : 0.530 5.599 18810 Z= 0.285 Chirality : 0.035 0.136 1944 Planarity : 0.005 0.045 2412 Dihedral : 4.057 15.725 1800 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.60 % Allowed : 22.43 % Favored : 74.96 % 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: 0.39 (0.21), residues: 1620 helix: 0.61 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.81 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP H 68 HIS 0.007 0.002 HIS G 51 PHE 0.012 0.001 PHE H 25 TYR 0.021 0.002 TYR M 32 ARG 0.009 0.001 ARG H 89 *********************** 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 485 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 448 time to evaluate : 1.660 Fit side-chains REVERT: G 81 ARG cc_start: 0.7564 (mmt180) cc_final: 0.6974 (ptp-170) REVERT: G 90 ASP cc_start: 0.7192 (t0) cc_final: 0.6909 (t0) REVERT: H 90 ASP cc_start: 0.7487 (t0) cc_final: 0.7187 (t0) REVERT: I 81 ARG cc_start: 0.7291 (mmt180) cc_final: 0.6530 (ptp-170) REVERT: I 90 ASP cc_start: 0.7472 (t0) cc_final: 0.7166 (t0) REVERT: J 31 ASP cc_start: 0.8102 (m-30) cc_final: 0.7714 (m-30) REVERT: J 62 ASN cc_start: 0.8866 (m-40) cc_final: 0.8446 (m110) REVERT: K 13 TYR cc_start: 0.8301 (m-10) cc_final: 0.7916 (m-10) REVERT: K 62 ASN cc_start: 0.8845 (m-40) cc_final: 0.8391 (m-40) REVERT: L 13 TYR cc_start: 0.8402 (m-10) cc_final: 0.8021 (m-10) REVERT: L 56 THR cc_start: 0.8913 (t) cc_final: 0.8599 (m) REVERT: L 62 ASN cc_start: 0.8808 (m-40) cc_final: 0.8351 (m-40) REVERT: L 70 MET cc_start: 0.8287 (mtm) cc_final: 0.7994 (mtm) REVERT: M 90 ASP cc_start: 0.7608 (t0) cc_final: 0.7398 (t0) REVERT: N 31 ASP cc_start: 0.8241 (m-30) cc_final: 0.7877 (m-30) REVERT: N 90 ASP cc_start: 0.7735 (t0) cc_final: 0.7301 (t0) REVERT: O 16 ASP cc_start: 0.8783 (t0) cc_final: 0.8453 (t0) REVERT: O 90 ASP cc_start: 0.7882 (t0) cc_final: 0.7433 (t0) REVERT: P 27 MET cc_start: 0.8362 (ttp) cc_final: 0.8154 (ttt) REVERT: P 90 ASP cc_start: 0.7616 (t0) cc_final: 0.7271 (t0) REVERT: Q 62 ASN cc_start: 0.8674 (m-40) cc_final: 0.8389 (m110) REVERT: Q 90 ASP cc_start: 0.7986 (t0) cc_final: 0.7472 (t0) REVERT: R 62 ASN cc_start: 0.8656 (m-40) cc_final: 0.7976 (m110) REVERT: R 90 ASP cc_start: 0.7504 (t0) cc_final: 0.7161 (t0) REVERT: S 27 MET cc_start: 0.8608 (ttp) cc_final: 0.8372 (ttt) REVERT: U 30 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7354 (mt-10) REVERT: U 31 ASP cc_start: 0.8001 (m-30) cc_final: 0.7691 (m-30) REVERT: U 35 GLN cc_start: 0.7356 (tm-30) cc_final: 0.7033 (tm-30) REVERT: U 47 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6703 (mm-30) REVERT: U 62 ASN cc_start: 0.8989 (m-40) cc_final: 0.8533 (m-40) REVERT: U 90 ASP cc_start: 0.7785 (t0) cc_final: 0.7581 (t0) REVERT: V 36 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7227 (mtpp) REVERT: V 85 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7435 (mt-10) REVERT: W 12 ARG cc_start: 0.7716 (mmm160) cc_final: 0.7383 (tpt90) REVERT: W 16 ASP cc_start: 0.8479 (t70) cc_final: 0.8088 (t0) REVERT: W 36 LYS cc_start: 0.7527 (mtpt) cc_final: 0.7222 (mtpt) REVERT: X 36 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7339 (mtpt) REVERT: X 90 ASP cc_start: 0.8179 (t0) cc_final: 0.7967 (t0) outliers start: 37 outliers final: 21 residues processed: 464 average time/residue: 0.3185 time to fit residues: 199.1853 Evaluate side-chains 460 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 437 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 36 LYS Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 56 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 56 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 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: 0.7980 chunk 39 optimal weight: 50.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.3822 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= 0.269 Angle : 0.555 5.118 18810 Z= 0.300 Chirality : 0.036 0.141 1944 Planarity : 0.005 0.046 2412 Dihedral : 4.194 16.091 1800 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.95 % Allowed : 23.77 % Favored : 73.28 % 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: 0.41 (0.20), residues: 1620 helix: 0.69 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.12 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 73 HIS 0.008 0.002 HIS G 51 PHE 0.016 0.002 PHE I 25 TYR 0.029 0.002 TYR M 32 ARG 0.010 0.001 ARG K 89 *********************** 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 490 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 448 time to evaluate : 1.555 Fit side-chains REVERT: G 81 ARG cc_start: 0.7555 (mmt180) cc_final: 0.6944 (mtp180) REVERT: H 90 ASP cc_start: 0.7701 (t0) cc_final: 0.7284 (t0) REVERT: I 81 ARG cc_start: 0.7352 (mmt180) cc_final: 0.6446 (ptp-170) REVERT: I 90 ASP cc_start: 0.7643 (t0) cc_final: 0.7354 (t0) REVERT: J 31 ASP cc_start: 0.8197 (m-30) cc_final: 0.7798 (m-30) REVERT: J 62 ASN cc_start: 0.8872 (m-40) cc_final: 0.8501 (m-40) REVERT: K 13 TYR cc_start: 0.8399 (m-10) cc_final: 0.7909 (m-10) REVERT: K 62 ASN cc_start: 0.8770 (m-40) cc_final: 0.8452 (m-40) REVERT: L 13 TYR cc_start: 0.8477 (m-10) cc_final: 0.7980 (m-10) REVERT: L 62 ASN cc_start: 0.8849 (m-40) cc_final: 0.8363 (m-40) REVERT: L 81 ARG cc_start: 0.7874 (mmt180) cc_final: 0.6650 (mtm110) REVERT: N 31 ASP cc_start: 0.8230 (m-30) cc_final: 0.7834 (m-30) REVERT: N 90 ASP cc_start: 0.7881 (t0) cc_final: 0.7439 (t0) REVERT: O 16 ASP cc_start: 0.8662 (t0) cc_final: 0.8261 (t0) REVERT: O 90 ASP cc_start: 0.7985 (t0) cc_final: 0.7513 (t0) REVERT: P 90 ASP cc_start: 0.7715 (t0) cc_final: 0.7318 (t0) REVERT: Q 27 MET cc_start: 0.8180 (ttt) cc_final: 0.7956 (ttt) REVERT: Q 62 ASN cc_start: 0.8780 (m-40) cc_final: 0.8440 (m110) REVERT: Q 90 ASP cc_start: 0.8067 (t0) cc_final: 0.7506 (t0) REVERT: R 62 ASN cc_start: 0.8731 (m-40) cc_final: 0.8115 (m110) REVERT: R 90 ASP cc_start: 0.7521 (t0) cc_final: 0.7181 (t0) REVERT: S 27 MET cc_start: 0.8607 (ttp) cc_final: 0.8389 (ttt) REVERT: S 85 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6686 (mt-10) REVERT: S 90 ASP cc_start: 0.8068 (t0) cc_final: 0.7713 (t0) REVERT: U 30 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7499 (mt-10) REVERT: U 31 ASP cc_start: 0.8053 (m-30) cc_final: 0.7716 (m-30) REVERT: U 35 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7158 (tm-30) REVERT: U 47 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6738 (mm-30) REVERT: U 62 ASN cc_start: 0.9064 (m-40) cc_final: 0.8611 (m-40) REVERT: V 36 LYS cc_start: 0.7828 (mttt) cc_final: 0.7366 (mtpp) REVERT: W 12 ARG cc_start: 0.7762 (mmm160) cc_final: 0.7416 (tpt90) REVERT: W 16 ASP cc_start: 0.8428 (t70) cc_final: 0.8092 (t0) REVERT: W 36 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7281 (mtpt) REVERT: W 91 GLU cc_start: 0.7989 (tt0) cc_final: 0.7625 (tt0) REVERT: X 36 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7509 (mtpt) REVERT: X 90 ASP cc_start: 0.8221 (t0) cc_final: 0.7919 (t0) outliers start: 42 outliers final: 31 residues processed: 468 average time/residue: 0.3236 time to fit residues: 202.4694 Evaluate side-chains 469 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 437 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 58 MET Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain S residue 56 THR Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 56 THR Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 56 THR Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 56 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 62 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13968 Z= 0.376 Angle : 0.616 5.733 18810 Z= 0.333 Chirality : 0.039 0.151 1944 Planarity : 0.006 0.046 2412 Dihedral : 4.461 16.131 1800 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.31 % Allowed : 24.19 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1620 helix: 0.51 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.14 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 73 HIS 0.008 0.002 HIS G 51 PHE 0.013 0.002 PHE I 25 TYR 0.030 0.002 TYR M 32 ARG 0.010 0.001 ARG J 89 *********************** 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 495 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 448 time to evaluate : 1.567 Fit side-chains REVERT: G 81 ARG cc_start: 0.7601 (mmt180) cc_final: 0.6856 (mtp180) REVERT: G 90 ASP cc_start: 0.7337 (t0) cc_final: 0.6895 (t0) REVERT: H 90 ASP cc_start: 0.7708 (t0) cc_final: 0.7237 (t0) REVERT: I 81 ARG cc_start: 0.7432 (mmt180) cc_final: 0.6501 (ptp-170) REVERT: I 90 ASP cc_start: 0.7886 (t0) cc_final: 0.7351 (t0) REVERT: J 31 ASP cc_start: 0.8152 (m-30) cc_final: 0.7798 (m-30) REVERT: J 62 ASN cc_start: 0.8962 (m-40) cc_final: 0.8532 (m110) REVERT: J 70 MET cc_start: 0.8428 (ttp) cc_final: 0.7984 (ttm) REVERT: K 13 TYR cc_start: 0.8454 (m-10) cc_final: 0.7923 (m-10) REVERT: K 62 ASN cc_start: 0.8850 (m110) cc_final: 0.8539 (m-40) REVERT: L 13 TYR cc_start: 0.8485 (m-10) cc_final: 0.7930 (m-10) REVERT: L 62 ASN cc_start: 0.8899 (m-40) cc_final: 0.8576 (m-40) REVERT: L 81 ARG cc_start: 0.7912 (mmt180) cc_final: 0.6731 (mtm110) REVERT: N 31 ASP cc_start: 0.8161 (m-30) cc_final: 0.7853 (m-30) REVERT: N 90 ASP cc_start: 0.7989 (t0) cc_final: 0.7513 (t0) REVERT: O 16 ASP cc_start: 0.8711 (t0) cc_final: 0.8258 (t0) REVERT: O 90 ASP cc_start: 0.8074 (t0) cc_final: 0.7520 (t0) REVERT: P 90 ASP cc_start: 0.7879 (t0) cc_final: 0.7400 (t0) REVERT: Q 27 MET cc_start: 0.8250 (ttt) cc_final: 0.8020 (ttt) REVERT: Q 62 ASN cc_start: 0.8807 (m-40) cc_final: 0.8466 (m110) REVERT: R 62 ASN cc_start: 0.8782 (m-40) cc_final: 0.8122 (m110) REVERT: R 88 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8315 (mtmt) REVERT: R 90 ASP cc_start: 0.7638 (t0) cc_final: 0.7200 (t0) REVERT: S 85 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6612 (mt-10) REVERT: S 90 ASP cc_start: 0.8278 (t0) cc_final: 0.8074 (t0) REVERT: U 30 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7431 (mt-10) REVERT: U 35 GLN cc_start: 0.7443 (tm-30) cc_final: 0.7076 (tm-30) REVERT: U 47 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6730 (mm-30) REVERT: U 62 ASN cc_start: 0.9092 (m-40) cc_final: 0.8578 (m-40) REVERT: U 90 ASP cc_start: 0.7882 (t0) cc_final: 0.7667 (t0) REVERT: V 32 TYR cc_start: 0.8505 (t80) cc_final: 0.8259 (t80) REVERT: V 36 LYS cc_start: 0.8052 (mttt) cc_final: 0.7431 (mtpp) REVERT: V 62 ASN cc_start: 0.9196 (m-40) cc_final: 0.8730 (m-40) REVERT: W 16 ASP cc_start: 0.8487 (t70) cc_final: 0.8165 (t0) REVERT: W 36 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7173 (mtpp) REVERT: X 36 LYS cc_start: 0.7826 (mttt) cc_final: 0.7547 (mtpt) REVERT: X 90 ASP cc_start: 0.8324 (t0) cc_final: 0.8010 (t0) outliers start: 47 outliers final: 34 residues processed: 469 average time/residue: 0.3302 time to fit residues: 205.8121 Evaluate side-chains 475 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 441 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 58 MET Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain S residue 56 THR Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 56 THR Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain X residue 56 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7876 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13968 Z= 0.173 Angle : 0.523 6.556 18810 Z= 0.281 Chirality : 0.034 0.132 1944 Planarity : 0.006 0.056 2412 Dihedral : 4.092 16.476 1800 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.76 % Allowed : 25.95 % Favored : 72.29 % 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: 0.81 (0.20), residues: 1620 helix: 1.02 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.18 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP H 68 HIS 0.010 0.002 HIS G 51 PHE 0.012 0.001 PHE H 25 TYR 0.023 0.002 TYR M 32 ARG 0.012 0.001 ARG J 89 *********************** 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 465 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 440 time to evaluate : 1.556 Fit side-chains REVERT: G 81 ARG cc_start: 0.7525 (mmt180) cc_final: 0.6887 (mtp180) REVERT: G 90 ASP cc_start: 0.7360 (t0) cc_final: 0.6836 (t0) REVERT: H 64 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7073 (mm-30) REVERT: H 90 ASP cc_start: 0.7699 (t0) cc_final: 0.7254 (t0) REVERT: I 90 ASP cc_start: 0.7764 (t0) cc_final: 0.7327 (t0) REVERT: J 31 ASP cc_start: 0.8156 (m-30) cc_final: 0.7777 (m-30) REVERT: J 62 ASN cc_start: 0.8826 (m-40) cc_final: 0.8358 (m110) REVERT: J 70 MET cc_start: 0.8336 (ttp) cc_final: 0.7781 (ttm) REVERT: K 13 TYR cc_start: 0.8355 (m-10) cc_final: 0.7872 (m-10) REVERT: K 62 ASN cc_start: 0.8705 (m110) cc_final: 0.8389 (m-40) REVERT: K 89 ARG cc_start: 0.8333 (mtm110) cc_final: 0.8125 (mtm110) REVERT: L 13 TYR cc_start: 0.8434 (m-10) cc_final: 0.8067 (m-10) REVERT: L 62 ASN cc_start: 0.8735 (m-40) cc_final: 0.8429 (m-40) REVERT: N 31 ASP cc_start: 0.8034 (m-30) cc_final: 0.7699 (m-30) REVERT: N 90 ASP cc_start: 0.7705 (t0) cc_final: 0.7311 (t0) REVERT: O 16 ASP cc_start: 0.8556 (t0) cc_final: 0.8196 (t0) REVERT: O 88 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8637 (ttpp) REVERT: O 90 ASP cc_start: 0.7907 (t0) cc_final: 0.7424 (t0) REVERT: P 90 ASP cc_start: 0.7631 (t0) cc_final: 0.7242 (t0) REVERT: Q 27 MET cc_start: 0.8190 (ttt) cc_final: 0.7916 (ttt) REVERT: Q 62 ASN cc_start: 0.8538 (m-40) cc_final: 0.8268 (m110) REVERT: Q 90 ASP cc_start: 0.8009 (t0) cc_final: 0.7308 (t0) REVERT: R 62 ASN cc_start: 0.8604 (m-40) cc_final: 0.7951 (m110) REVERT: R 88 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8231 (mtmt) REVERT: R 90 ASP cc_start: 0.7527 (t0) cc_final: 0.7123 (t0) REVERT: S 47 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6764 (mm-30) REVERT: S 70 MET cc_start: 0.8000 (mtp) cc_final: 0.7798 (mtp) REVERT: S 85 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6608 (mt-10) REVERT: T 47 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6967 (mm-30) REVERT: T 90 ASP cc_start: 0.7954 (t0) cc_final: 0.7617 (t0) REVERT: U 31 ASP cc_start: 0.7992 (m-30) cc_final: 0.7785 (m-30) REVERT: U 47 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6774 (mm-30) REVERT: U 62 ASN cc_start: 0.8950 (m-40) cc_final: 0.8548 (m-40) REVERT: U 90 ASP cc_start: 0.7823 (t0) cc_final: 0.7590 (t0) REVERT: V 32 TYR cc_start: 0.8390 (t80) cc_final: 0.8136 (t80) REVERT: V 36 LYS cc_start: 0.7883 (mttt) cc_final: 0.7368 (mtpp) REVERT: V 85 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7377 (mt-10) REVERT: W 12 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7344 (tpt90) REVERT: W 16 ASP cc_start: 0.8307 (t70) cc_final: 0.8077 (t0) REVERT: W 36 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7009 (mtpp) REVERT: X 36 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7218 (mtpt) REVERT: X 90 ASP cc_start: 0.8192 (t0) cc_final: 0.7898 (t0) outliers start: 25 outliers final: 17 residues processed: 447 average time/residue: 0.3247 time to fit residues: 193.6962 Evaluate side-chains 447 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 429 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 36 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13968 Z= 0.305 Angle : 0.579 6.880 18810 Z= 0.313 Chirality : 0.037 0.152 1944 Planarity : 0.006 0.056 2412 Dihedral : 4.261 16.269 1800 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.11 % Allowed : 26.58 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1620 helix: 0.84 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 73 HIS 0.009 0.002 HIS G 51 PHE 0.016 0.001 PHE I 25 TYR 0.027 0.002 TYR M 32 ARG 0.014 0.001 ARG J 89 *********************** 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 475 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 445 time to evaluate : 1.573 Fit side-chains REVERT: G 81 ARG cc_start: 0.7547 (mmt180) cc_final: 0.6832 (mtp180) REVERT: G 90 ASP cc_start: 0.7579 (t0) cc_final: 0.7031 (t0) REVERT: H 90 ASP cc_start: 0.7858 (t0) cc_final: 0.7360 (t0) REVERT: I 81 ARG cc_start: 0.7323 (mmt180) cc_final: 0.6469 (ptp-170) REVERT: I 90 ASP cc_start: 0.7884 (t0) cc_final: 0.7450 (t0) REVERT: J 13 TYR cc_start: 0.8222 (m-10) cc_final: 0.7876 (m-10) REVERT: J 31 ASP cc_start: 0.8080 (m-30) cc_final: 0.7727 (m-30) REVERT: J 62 ASN cc_start: 0.8924 (m-40) cc_final: 0.8491 (m110) REVERT: J 70 MET cc_start: 0.8382 (ttp) cc_final: 0.7797 (ttm) REVERT: K 13 TYR cc_start: 0.8398 (m-10) cc_final: 0.7841 (m-10) REVERT: K 62 ASN cc_start: 0.8823 (m110) cc_final: 0.8502 (m-40) REVERT: L 13 TYR cc_start: 0.8494 (m-10) cc_final: 0.7971 (m-10) REVERT: L 62 ASN cc_start: 0.8810 (m-40) cc_final: 0.8404 (m-40) REVERT: L 81 ARG cc_start: 0.7870 (mmt180) cc_final: 0.6731 (mtm110) REVERT: N 31 ASP cc_start: 0.8079 (m-30) cc_final: 0.7818 (m-30) REVERT: N 90 ASP cc_start: 0.7929 (t0) cc_final: 0.7487 (t0) REVERT: O 16 ASP cc_start: 0.8559 (t0) cc_final: 0.8187 (t0) REVERT: O 90 ASP cc_start: 0.8007 (t0) cc_final: 0.7483 (t0) REVERT: P 90 ASP cc_start: 0.7849 (t0) cc_final: 0.7400 (t0) REVERT: Q 27 MET cc_start: 0.8222 (ttt) cc_final: 0.7979 (ttt) REVERT: Q 62 ASN cc_start: 0.8718 (m-40) cc_final: 0.8358 (m110) REVERT: Q 90 ASP cc_start: 0.8100 (t0) cc_final: 0.7591 (t0) REVERT: R 62 ASN cc_start: 0.8889 (m-40) cc_final: 0.8142 (m-40) REVERT: R 90 ASP cc_start: 0.7627 (t0) cc_final: 0.7225 (t0) REVERT: S 85 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6563 (mt-10) REVERT: S 90 ASP cc_start: 0.8088 (t0) cc_final: 0.7778 (t0) REVERT: T 47 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6885 (mm-30) REVERT: U 31 ASP cc_start: 0.8145 (m-30) cc_final: 0.7941 (m-30) REVERT: U 35 GLN cc_start: 0.7354 (tm-30) cc_final: 0.6960 (tm-30) REVERT: U 47 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6767 (mm-30) REVERT: U 62 ASN cc_start: 0.9031 (m-40) cc_final: 0.8605 (m-40) REVERT: U 90 ASP cc_start: 0.7894 (t0) cc_final: 0.7676 (t0) REVERT: V 27 MET cc_start: 0.8543 (ttp) cc_final: 0.8321 (ttt) REVERT: V 32 TYR cc_start: 0.8454 (t80) cc_final: 0.8181 (t80) REVERT: V 36 LYS cc_start: 0.7940 (mttt) cc_final: 0.7355 (mtpp) REVERT: W 12 ARG cc_start: 0.7793 (mmm160) cc_final: 0.7463 (tpt90) REVERT: W 16 ASP cc_start: 0.8373 (t70) cc_final: 0.8125 (t0) REVERT: W 36 LYS cc_start: 0.7632 (mtpt) cc_final: 0.7060 (mtpp) REVERT: X 36 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7568 (mtpt) REVERT: X 90 ASP cc_start: 0.8341 (t0) cc_final: 0.8058 (t0) outliers start: 30 outliers final: 23 residues processed: 456 average time/residue: 0.3339 time to fit residues: 202.6172 Evaluate side-chains 466 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 442 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 58 MET Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain S residue 59 ILE Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 36 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7880 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13968 Z= 0.186 Angle : 0.542 8.811 18810 Z= 0.292 Chirality : 0.034 0.155 1944 Planarity : 0.006 0.064 2412 Dihedral : 4.056 16.272 1800 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.27 % Allowed : 27.57 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1620 helix: 1.12 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.23 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP H 68 HIS 0.009 0.001 HIS G 51 PHE 0.014 0.001 PHE I 25 TYR 0.022 0.002 TYR M 32 ARG 0.015 0.001 ARG K 89 *********************** 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 454 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 436 time to evaluate : 1.617 Fit side-chains REVERT: G 81 ARG cc_start: 0.7500 (mmt180) cc_final: 0.6908 (mtp180) REVERT: H 90 ASP cc_start: 0.7825 (t0) cc_final: 0.7378 (t0) REVERT: I 90 ASP cc_start: 0.7826 (t0) cc_final: 0.7452 (t0) REVERT: J 31 ASP cc_start: 0.8163 (m-30) cc_final: 0.7768 (m-30) REVERT: J 62 ASN cc_start: 0.8832 (m-40) cc_final: 0.8398 (m110) REVERT: J 70 MET cc_start: 0.8462 (ttp) cc_final: 0.7844 (ttm) REVERT: J 90 ASP cc_start: 0.7094 (t0) cc_final: 0.6694 (t0) REVERT: K 13 TYR cc_start: 0.8374 (m-10) cc_final: 0.7901 (m-10) REVERT: K 62 ASN cc_start: 0.8724 (m110) cc_final: 0.8413 (m-40) REVERT: L 13 TYR cc_start: 0.8450 (m-10) cc_final: 0.8086 (m-10) REVERT: L 16 ASP cc_start: 0.8672 (t0) cc_final: 0.8445 (t0) REVERT: L 62 ASN cc_start: 0.8749 (m-40) cc_final: 0.8481 (m-40) REVERT: N 31 ASP cc_start: 0.7973 (m-30) cc_final: 0.7708 (m-30) REVERT: N 90 ASP cc_start: 0.7741 (t0) cc_final: 0.7270 (t0) REVERT: O 16 ASP cc_start: 0.8596 (t0) cc_final: 0.8183 (t0) REVERT: O 90 ASP cc_start: 0.7969 (t0) cc_final: 0.7429 (t0) REVERT: P 90 ASP cc_start: 0.7675 (t0) cc_final: 0.7324 (t0) REVERT: Q 27 MET cc_start: 0.8142 (ttt) cc_final: 0.7910 (ttt) REVERT: Q 31 ASP cc_start: 0.8212 (m-30) cc_final: 0.7985 (m-30) REVERT: Q 62 ASN cc_start: 0.8630 (m-40) cc_final: 0.8342 (m110) REVERT: Q 90 ASP cc_start: 0.8030 (t0) cc_final: 0.7375 (t0) REVERT: R 62 ASN cc_start: 0.8811 (m-40) cc_final: 0.8243 (m-40) REVERT: R 88 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8234 (mtmt) REVERT: R 90 ASP cc_start: 0.7573 (t0) cc_final: 0.7159 (t0) REVERT: S 47 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6827 (mm-30) REVERT: S 85 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6583 (mt-10) REVERT: S 90 ASP cc_start: 0.8138 (t0) cc_final: 0.7832 (t0) REVERT: T 47 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7058 (mm-30) REVERT: T 90 ASP cc_start: 0.7973 (t0) cc_final: 0.7661 (t0) REVERT: U 47 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6643 (mm-30) REVERT: U 62 ASN cc_start: 0.8955 (m-40) cc_final: 0.8562 (m-40) REVERT: V 27 MET cc_start: 0.8484 (ttp) cc_final: 0.8246 (ttt) REVERT: V 36 LYS cc_start: 0.7870 (mttt) cc_final: 0.7393 (mtpp) REVERT: V 85 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7379 (mt-10) REVERT: W 12 ARG cc_start: 0.7635 (mmm160) cc_final: 0.7347 (tpt90) REVERT: W 36 LYS cc_start: 0.7568 (mtpt) cc_final: 0.7005 (mtpp) REVERT: X 36 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7451 (mtpt) REVERT: X 90 ASP cc_start: 0.8275 (t0) cc_final: 0.8018 (t0) outliers start: 18 outliers final: 15 residues processed: 442 average time/residue: 0.3404 time to fit residues: 200.4885 Evaluate side-chains 440 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 424 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 47 GLU 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: 0.0170 chunk 72 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13968 Z= 0.178 Angle : 0.539 7.476 18810 Z= 0.290 Chirality : 0.034 0.149 1944 Planarity : 0.005 0.060 2412 Dihedral : 3.876 15.958 1800 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.05 % Allowed : 28.06 % Favored : 70.89 % 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: 1.08 (0.21), residues: 1620 helix: 1.20 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP H 68 HIS 0.009 0.001 HIS G 51 PHE 0.014 0.001 PHE H 25 TYR 0.019 0.002 TYR M 32 ARG 0.014 0.001 ARG K 89 ********************** 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 448 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 433 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7503 (mmt180) cc_final: 0.6921 (mtp180) REVERT: H 64 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6900 (mm-30) REVERT: H 90 ASP cc_start: 0.7792 (t0) cc_final: 0.7409 (t0) REVERT: I 90 ASP cc_start: 0.7863 (t0) cc_final: 0.7578 (t0) REVERT: J 31 ASP cc_start: 0.8128 (m-30) cc_final: 0.7748 (m-30) REVERT: J 62 ASN cc_start: 0.8813 (m-40) cc_final: 0.8390 (m110) REVERT: J 70 MET cc_start: 0.8469 (ttp) cc_final: 0.7818 (ttm) REVERT: J 90 ASP cc_start: 0.7111 (t0) cc_final: 0.6719 (t0) REVERT: K 13 TYR cc_start: 0.8328 (m-10) cc_final: 0.7969 (m-10) REVERT: K 62 ASN cc_start: 0.8707 (m110) cc_final: 0.8393 (m-40) REVERT: K 85 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6943 (tm-30) REVERT: L 13 TYR cc_start: 0.8414 (m-10) cc_final: 0.8110 (m-10) REVERT: N 90 ASP cc_start: 0.7687 (t0) cc_final: 0.7349 (t0) REVERT: O 16 ASP cc_start: 0.8513 (t0) cc_final: 0.8110 (t0) REVERT: O 90 ASP cc_start: 0.7928 (t0) cc_final: 0.7434 (t0) REVERT: P 90 ASP cc_start: 0.7574 (t0) cc_final: 0.7221 (t0) REVERT: Q 27 MET cc_start: 0.8100 (ttt) cc_final: 0.7857 (ttt) REVERT: Q 31 ASP cc_start: 0.8205 (m-30) cc_final: 0.7976 (m-30) REVERT: Q 62 ASN cc_start: 0.8598 (m-40) cc_final: 0.8291 (m110) REVERT: Q 90 ASP cc_start: 0.7985 (t0) cc_final: 0.7423 (t0) REVERT: R 62 ASN cc_start: 0.8678 (m110) cc_final: 0.8222 (m-40) REVERT: R 90 ASP cc_start: 0.7535 (t0) cc_final: 0.7144 (t0) REVERT: S 47 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6779 (mm-30) REVERT: S 85 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6601 (mt-10) REVERT: S 90 ASP cc_start: 0.8149 (t0) cc_final: 0.7945 (t0) REVERT: U 47 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6749 (mm-30) REVERT: U 62 ASN cc_start: 0.8913 (m-40) cc_final: 0.8627 (m-40) REVERT: V 27 MET cc_start: 0.8380 (ttp) cc_final: 0.8147 (ttt) REVERT: V 36 LYS cc_start: 0.7754 (mttt) cc_final: 0.7258 (mtpp) REVERT: W 12 ARG cc_start: 0.7583 (mmm160) cc_final: 0.7315 (tpt90) REVERT: W 36 LYS cc_start: 0.7456 (mtpt) cc_final: 0.7014 (mtpp) REVERT: X 36 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7361 (mtpt) REVERT: X 90 ASP cc_start: 0.8297 (t0) cc_final: 0.8092 (t0) outliers start: 15 outliers final: 13 residues processed: 439 average time/residue: 0.3260 time to fit residues: 190.9227 Evaluate side-chains 436 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 422 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 36 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0670 chunk 39 optimal weight: 0.0770 chunk 118 optimal weight: 0.0070 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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** L 45 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110838 restraints weight = 17750.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114634 restraints weight = 10249.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117361 restraints weight = 6822.692| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13968 Z= 0.171 Angle : 0.533 7.574 18810 Z= 0.287 Chirality : 0.034 0.136 1944 Planarity : 0.005 0.061 2412 Dihedral : 3.748 15.867 1800 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.13 % Allowed : 27.92 % Favored : 70.96 % 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: 1.29 (0.21), residues: 1620 helix: 1.31 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP H 68 HIS 0.010 0.001 HIS G 51 PHE 0.017 0.001 PHE I 25 TYR 0.018 0.002 TYR O 32 ARG 0.014 0.001 ARG H 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.90 seconds wall clock time: 63 minutes 17.27 seconds (3797.27 seconds total)