Starting phenix.real_space_refine on Fri Mar 15 03:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/03_2024/8j62_35999.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/03_2024/8j62_35999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/03_2024/8j62_35999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/03_2024/8j62_35999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/03_2024/8j62_35999.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/03_2024/8j62_35999.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 36 5.49 5 S 48 5.16 5 C 6578 2.51 5 N 1826 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "I GLU 45": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10448 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1521 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain: "C" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1075 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 844 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 912 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 480 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "X" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 5} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1521 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain: "G" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1075 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 844 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 912 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 480 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "Y" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 5} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 749 SG CYS A 84 32.319 53.134 49.548 1.00 41.85 S ATOM 771 SG CYS A 87 33.682 51.225 51.830 1.00 42.44 S ATOM 5972 SG CYS B 84 53.195 56.249 49.540 1.00 41.91 S ATOM 5994 SG CYS B 87 51.833 58.158 51.823 1.00 42.61 S Time building chain proxies: 6.00, per 1000 atoms: 0.57 Number of scatterers: 10448 At special positions: 0 Unit cell: (86.0096, 109.933, 105.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 48 16.00 P 36 15.00 O 1958 8.00 N 1826 7.00 C 6578 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: 4.08 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 87 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 84 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 84 " 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 35.9% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.656A pdb=" N LYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'C' and resid 14 through 31 Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.566A pdb=" N SER C 46 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'D' and resid 18 through 24 removed outlier: 3.898A pdb=" N GLU D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'E' and resid 14 through 31 Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.516A pdb=" N GLU E 45 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 111 removed outlier: 3.659A pdb=" N GLN E 105 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.556A pdb=" N LEU E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 51 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.656A pdb=" N LYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'G' and resid 14 through 31 Processing helix chain 'G' and resid 42 through 46 removed outlier: 3.566A pdb=" N SER G 46 " --> pdb=" O HIS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 111 Processing helix chain 'G' and resid 165 through 171 Processing helix chain 'H' and resid 18 through 24 removed outlier: 3.898A pdb=" N GLU H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 50 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'I' and resid 14 through 31 Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.516A pdb=" N GLU I 45 " --> pdb=" O HIS I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 111 removed outlier: 3.659A pdb=" N GLN I 105 " --> pdb=" O ASP I 101 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 171 removed outlier: 3.558A pdb=" N LEU I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 51 Processing helix chain 'J' and resid 70 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.897A pdb=" N TRP A 81 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 41 removed outlier: 4.876A pdb=" N ILE C 87 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE C 9 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 11.423A pdb=" N TRP C 89 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 14.227A pdb=" N VAL C 7 " --> pdb=" O TRP C 89 " (cutoff:3.500A) removed outlier: 18.909A pdb=" N LYS C 91 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 21.500A pdb=" N TRP C 5 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU D 64 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 55 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP D 120 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 41 removed outlier: 11.324A pdb=" N SER C 95 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE D 102 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.586A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU E 64 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG E 90 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE E 66 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU E 88 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR E 68 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP E 70 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY E 84 " --> pdb=" O TRP E 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.586A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU E 64 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG E 90 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE E 66 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU E 88 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR E 68 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP E 70 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY E 84 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN E 83 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE E 87 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 9 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 96 through 103 Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.898A pdb=" N TRP B 81 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41 removed outlier: 4.877A pdb=" N ILE G 87 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE G 9 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N TRP G 89 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 14.228A pdb=" N VAL G 7 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 18.909A pdb=" N LYS G 91 " --> pdb=" O TRP G 5 " (cutoff:3.500A) removed outlier: 21.500A pdb=" N TRP G 5 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU H 64 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE H 55 " --> pdb=" O PHE H 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP H 120 " --> pdb=" O ASP H 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 39 through 41 removed outlier: 11.323A pdb=" N SER G 95 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE H 102 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 39 through 41 removed outlier: 6.585A pdb=" N THR I 68 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU I 54 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE I 66 " --> pdb=" O GLU I 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS I 56 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 64 " --> pdb=" O HIS I 56 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU I 64 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG I 90 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE I 66 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU I 88 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR I 68 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER I 86 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP I 70 " --> pdb=" O GLY I 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY I 84 " --> pdb=" O TRP I 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 39 through 41 removed outlier: 6.585A pdb=" N THR I 68 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU I 54 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE I 66 " --> pdb=" O GLU I 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS I 56 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 64 " --> pdb=" O HIS I 56 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU I 64 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG I 90 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE I 66 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU I 88 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR I 68 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER I 86 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP I 70 " --> pdb=" O GLY I 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY I 84 " --> pdb=" O TRP I 70 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE I 87 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE I 9 " --> pdb=" O ILE I 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 96 through 103 582 hydrogen bonds defined for protein. 1566 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: 3.09 Time building geometry restraints manager: 4.28 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: 3012 1.34 - 1.45: 2237 1.45 - 1.57: 5425 1.57 - 1.69: 72 1.69 - 1.81: 76 Bond restraints: 10822 Sorted by residual: bond pdb=" CA TYR D 85 " pdb=" CB TYR D 85 " ideal model delta sigma weight residual 1.535 1.552 -0.017 2.09e-02 2.29e+03 6.29e-01 bond pdb=" CA TYR H 85 " pdb=" CB TYR H 85 " ideal model delta sigma weight residual 1.535 1.551 -0.016 2.09e-02 2.29e+03 5.61e-01 bond pdb=" CA GLY I 82 " pdb=" C GLY I 82 " ideal model delta sigma weight residual 1.522 1.515 0.007 1.06e-02 8.90e+03 4.67e-01 bond pdb=" CA GLY E 82 " pdb=" C GLY E 82 " ideal model delta sigma weight residual 1.522 1.515 0.007 1.06e-02 8.90e+03 4.47e-01 bond pdb=" CB GLU A 163 " pdb=" CG GLU A 163 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.15e-01 ... (remaining 10817 not shown) Histogram of bond angle deviations from ideal: 100.71 - 107.41: 708 107.41 - 114.10: 5955 114.10 - 120.79: 4441 120.79 - 127.48: 3499 127.48 - 134.18: 251 Bond angle restraints: 14854 Sorted by residual: angle pdb=" C VAL H 86 " pdb=" N ASP H 87 " pdb=" CA ASP H 87 " ideal model delta sigma weight residual 121.75 118.21 3.54 1.73e+00 3.34e-01 4.19e+00 angle pdb=" C3' U Y 11 " pdb=" O3' U Y 11 " pdb=" P U Y 12 " ideal model delta sigma weight residual 120.20 123.24 -3.04 1.50e+00 4.44e-01 4.11e+00 angle pdb=" C VAL D 86 " pdb=" N ASP D 87 " pdb=" CA ASP D 87 " ideal model delta sigma weight residual 121.75 118.25 3.50 1.73e+00 3.34e-01 4.08e+00 angle pdb=" C3' U X 11 " pdb=" O3' U X 11 " pdb=" P U X 12 " ideal model delta sigma weight residual 120.20 123.22 -3.02 1.50e+00 4.44e-01 4.06e+00 angle pdb=" C HIS I 28 " pdb=" N MET I 29 " pdb=" CA MET I 29 " ideal model delta sigma weight residual 121.66 118.60 3.06 1.76e+00 3.23e-01 3.03e+00 ... (remaining 14849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 5926 32.69 - 65.37: 356 65.37 - 98.06: 26 98.06 - 130.74: 0 130.74 - 163.43: 2 Dihedral angle restraints: 6310 sinusoidal: 2858 harmonic: 3452 Sorted by residual: dihedral pdb=" O4' C Y 1 " pdb=" C1' C Y 1 " pdb=" N1 C Y 1 " pdb=" C2 C Y 1 " ideal model delta sinusoidal sigma weight residual 200.00 36.57 163.43 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' C X 1 " pdb=" C1' C X 1 " pdb=" N1 C X 1 " pdb=" C2 C X 1 " ideal model delta sinusoidal sigma weight residual 200.00 36.64 163.36 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" CB GLU I 54 " pdb=" CG GLU I 54 " pdb=" CD GLU I 54 " pdb=" OE1 GLU I 54 " ideal model delta sinusoidal sigma weight residual 0.00 -90.15 90.15 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 6307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 961 0.027 - 0.053: 372 0.053 - 0.080: 126 0.080 - 0.106: 95 0.106 - 0.133: 40 Chirality restraints: 1594 Sorted by residual: chirality pdb=" CA ILE I 57 " pdb=" N ILE I 57 " pdb=" C ILE I 57 " pdb=" CB ILE I 57 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE I 66 " pdb=" N ILE I 66 " pdb=" C ILE I 66 " pdb=" CB ILE I 66 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE E 57 " pdb=" N ILE E 57 " pdb=" C ILE E 57 " pdb=" CB ILE E 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1591 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 113 " -0.011 2.00e-02 2.50e+03 1.21e-02 3.66e+00 pdb=" CG TRP F 113 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP F 113 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP F 113 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 113 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 113 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 113 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 113 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 113 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 113 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 113 " 0.011 2.00e-02 2.50e+03 1.18e-02 3.50e+00 pdb=" CG TRP J 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP J 113 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP J 113 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 113 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 113 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 113 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 113 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 86 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00 pdb=" C VAL H 86 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL H 86 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP H 87 " 0.006 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1205 2.75 - 3.29: 9360 3.29 - 3.83: 18363 3.83 - 4.36: 22026 4.36 - 4.90: 37780 Nonbonded interactions: 88734 Sorted by model distance: nonbonded pdb=" OG SER H 53 " pdb=" O6 G Y 10 " model vdw 2.216 2.440 nonbonded pdb=" OG SER D 53 " pdb=" O6 G X 10 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR A 112 " pdb=" OP1 U X 8 " model vdw 2.226 2.440 nonbonded pdb=" OH TYR B 112 " pdb=" OP1 U Y 8 " model vdw 2.227 2.440 nonbonded pdb=" NH2 ARG G 23 " pdb=" OP2 C Y 17 " model vdw 2.239 2.520 ... (remaining 88729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 22 or (resid 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 60 or (resid 61 throug \ h 62 and (name N or name CA or name C or name O or name CB )) or resid 63 throug \ h 74 or resid 80 through 111 or resid 161 through 166 or (resid 167 through 168 \ and (name N or name CA or name C or name O or name CB )) or resid 169 through 17 \ 2)) selection = (chain 'E' and (resid 8 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 172)) selection = (chain 'G' and (resid 8 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 22 or (resid 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 60 or (resid 61 throug \ h 62 and (name N or name CA or name C or name O or name CB )) or resid 63 throug \ h 74 or resid 80 through 111 or resid 161 through 166 or (resid 167 through 168 \ and (name N or name CA or name C or name O or name CB )) or resid 169 through 17 \ 2)) selection = (chain 'I' and (resid 8 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 172)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'X' selection = chain 'Y' } 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 individual isotropic 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.930 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 33.710 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.002 0.020 10822 Z= 0.118 Angle : 0.464 6.001 14854 Z= 0.252 Chirality : 0.041 0.133 1594 Planarity : 0.003 0.027 1728 Dihedral : 18.883 163.427 4070 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.91 % Allowed : 24.35 % Favored : 72.75 % 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: 1.53 (0.25), residues: 1130 helix: 1.85 (0.28), residues: 352 sheet: 0.51 (0.27), residues: 326 loop : 0.93 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 113 HIS 0.002 0.000 HIS H 37 PHE 0.007 0.001 PHE A 58 TYR 0.014 0.001 TYR D 85 ARG 0.006 0.000 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 323 time to evaluate : 1.165 Fit side-chains REVERT: C 99 ASP cc_start: 0.7721 (p0) cc_final: 0.7166 (p0) REVERT: E 88 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7088 (tm-30) REVERT: H 21 LEU cc_start: 0.8074 (mp) cc_final: 0.7857 (mp) outliers start: 29 outliers final: 16 residues processed: 341 average time/residue: 1.3469 time to fit residues: 488.3770 Evaluate side-chains 277 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 114 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 30 optimal weight: 0.0270 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.0770 chunk 105 optimal weight: 9.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 43 HIS ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN G 43 HIS ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10822 Z= 0.297 Angle : 0.566 5.793 14854 Z= 0.300 Chirality : 0.045 0.157 1594 Planarity : 0.004 0.032 1728 Dihedral : 15.120 167.772 1868 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.51 % Allowed : 27.35 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1130 helix: 1.73 (0.26), residues: 374 sheet: 0.59 (0.27), residues: 328 loop : 1.08 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 113 HIS 0.004 0.001 HIS G 43 PHE 0.008 0.002 PHE D 57 TYR 0.017 0.001 TYR J 29 ARG 0.007 0.001 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 249 time to evaluate : 1.158 Fit side-chains REVERT: A 57 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7543 (ttm110) REVERT: A 166 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: C 91 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8214 (tppp) REVERT: E 17 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.6907 (mtt180) REVERT: E 88 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: B 166 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: H 122 MET cc_start: 0.8400 (mmp) cc_final: 0.8019 (mmp) REVERT: I 17 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.6917 (mtt180) REVERT: I 88 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6866 (tm-30) outliers start: 55 outliers final: 24 residues processed: 281 average time/residue: 1.3517 time to fit residues: 404.4214 Evaluate side-chains 269 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN H 45 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10822 Z= 0.148 Angle : 0.521 8.426 14854 Z= 0.270 Chirality : 0.042 0.165 1594 Planarity : 0.004 0.029 1728 Dihedral : 14.934 166.085 1854 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.61 % Allowed : 27.56 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.25), residues: 1130 helix: 2.01 (0.27), residues: 374 sheet: 0.74 (0.27), residues: 330 loop : 1.10 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 113 HIS 0.003 0.001 HIS G 43 PHE 0.006 0.001 PHE F 57 TYR 0.009 0.001 TYR C 69 ARG 0.007 0.001 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7421 (m110) REVERT: A 166 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: E 88 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7114 (tm-30) outliers start: 46 outliers final: 21 residues processed: 281 average time/residue: 1.3567 time to fit residues: 405.4451 Evaluate side-chains 269 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN D 67 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN G 110 HIS H 45 GLN H 67 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 10822 Z= 0.575 Angle : 0.687 7.671 14854 Z= 0.359 Chirality : 0.050 0.169 1594 Planarity : 0.005 0.037 1728 Dihedral : 15.331 171.688 1854 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 7.21 % Allowed : 27.35 % Favored : 65.43 % 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: 1.49 (0.25), residues: 1130 helix: 1.68 (0.26), residues: 378 sheet: 0.47 (0.27), residues: 326 loop : 1.01 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 89 HIS 0.005 0.001 HIS G 56 PHE 0.014 0.002 PHE A 140 TYR 0.022 0.002 TYR F 29 ARG 0.008 0.001 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 249 time to evaluate : 1.193 Fit side-chains REVERT: A 1 MET cc_start: 0.8609 (ttp) cc_final: 0.8394 (ttt) REVERT: A 57 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7714 (ttm110) REVERT: A 166 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: E 88 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: B 166 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: G 88 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7004 (pt0) REVERT: I 88 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6996 (tm-30) outliers start: 72 outliers final: 37 residues processed: 291 average time/residue: 1.3190 time to fit residues: 409.0015 Evaluate side-chains 279 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 110 HIS ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10822 Z= 0.169 Angle : 0.576 9.982 14854 Z= 0.292 Chirality : 0.042 0.148 1594 Planarity : 0.004 0.037 1728 Dihedral : 15.108 169.218 1854 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.91 % Allowed : 30.96 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1130 helix: 1.97 (0.27), residues: 364 sheet: 0.51 (0.27), residues: 328 loop : 0.98 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 89 HIS 0.003 0.001 HIS G 110 PHE 0.007 0.001 PHE A 113 TYR 0.009 0.001 TYR G 69 ARG 0.009 0.001 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 1.256 Fit side-chains REVERT: A 136 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7443 (m110) REVERT: A 166 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: E 17 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7715 (mtt180) REVERT: E 88 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6859 (tm-30) REVERT: E 171 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: B 166 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: G 99 ASP cc_start: 0.7878 (p0) cc_final: 0.7104 (p0) REVERT: I 88 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7024 (tm-30) outliers start: 39 outliers final: 18 residues processed: 272 average time/residue: 1.4290 time to fit residues: 412.6950 Evaluate side-chains 275 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 251 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN H 67 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10822 Z= 0.329 Angle : 0.623 9.756 14854 Z= 0.317 Chirality : 0.045 0.149 1594 Planarity : 0.004 0.049 1728 Dihedral : 15.181 170.511 1854 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.71 % Allowed : 28.76 % Favored : 65.53 % 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: 1.59 (0.25), residues: 1130 helix: 1.84 (0.26), residues: 376 sheet: 0.48 (0.27), residues: 326 loop : 1.03 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 89 HIS 0.006 0.001 HIS G 110 PHE 0.009 0.001 PHE H 57 TYR 0.022 0.001 TYR J 29 ARG 0.010 0.001 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 245 time to evaluate : 1.182 Fit side-chains REVERT: A 57 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7581 (ttm110) REVERT: A 136 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7562 (m110) REVERT: A 166 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: E 88 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: B 166 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: G 88 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6974 (pt0) REVERT: I 88 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7032 (tm-30) outliers start: 57 outliers final: 30 residues processed: 280 average time/residue: 1.3277 time to fit residues: 395.9539 Evaluate side-chains 275 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN H 67 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10822 Z= 0.270 Angle : 0.618 8.964 14854 Z= 0.312 Chirality : 0.044 0.143 1594 Planarity : 0.004 0.054 1728 Dihedral : 15.174 170.731 1854 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.01 % Allowed : 30.56 % Favored : 64.43 % 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: 1.57 (0.25), residues: 1130 helix: 1.88 (0.26), residues: 374 sheet: 0.51 (0.28), residues: 324 loop : 0.92 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 89 HIS 0.008 0.001 HIS G 110 PHE 0.008 0.001 PHE D 68 TYR 0.009 0.001 TYR G 69 ARG 0.011 0.001 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 244 time to evaluate : 1.212 Fit side-chains REVERT: A 57 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7511 (ttm110) REVERT: A 136 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7542 (m110) REVERT: A 166 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: D 54 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: E 88 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: B 166 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: G 88 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: I 88 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7039 (tm-30) outliers start: 50 outliers final: 31 residues processed: 279 average time/residue: 1.3245 time to fit residues: 393.9439 Evaluate side-chains 276 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10822 Z= 0.283 Angle : 0.634 9.440 14854 Z= 0.319 Chirality : 0.044 0.142 1594 Planarity : 0.004 0.057 1728 Dihedral : 15.190 170.734 1854 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.41 % Allowed : 31.06 % Favored : 64.53 % 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: 1.58 (0.25), residues: 1130 helix: 1.97 (0.27), residues: 362 sheet: 0.50 (0.28), residues: 324 loop : 0.90 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 89 HIS 0.006 0.001 HIS G 110 PHE 0.010 0.001 PHE J 69 TYR 0.023 0.001 TYR F 29 ARG 0.013 0.001 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 242 time to evaluate : 1.123 Fit side-chains REVERT: A 57 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7538 (ttm110) REVERT: A 136 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7512 (m110) REVERT: A 166 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: D 54 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: E 88 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: B 166 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: G 88 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6946 (pt0) REVERT: H 54 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: I 88 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7046 (tm-30) outliers start: 44 outliers final: 31 residues processed: 275 average time/residue: 1.3273 time to fit residues: 388.3281 Evaluate side-chains 278 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 238 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 0.1980 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10822 Z= 0.194 Angle : 0.627 11.279 14854 Z= 0.311 Chirality : 0.043 0.138 1594 Planarity : 0.005 0.059 1728 Dihedral : 15.094 170.596 1854 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.91 % Allowed : 31.86 % Favored : 64.23 % 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: 1.67 (0.26), residues: 1130 helix: 2.13 (0.28), residues: 362 sheet: 0.50 (0.28), residues: 324 loop : 0.91 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 89 HIS 0.006 0.001 HIS G 110 PHE 0.007 0.001 PHE J 69 TYR 0.010 0.001 TYR D 96 ARG 0.013 0.001 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 245 time to evaluate : 1.153 Fit side-chains REVERT: A 136 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7389 (m110) REVERT: E 17 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7775 (mtt180) REVERT: E 88 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: I 88 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7072 (tm-30) outliers start: 39 outliers final: 26 residues processed: 272 average time/residue: 1.3183 time to fit residues: 382.5452 Evaluate side-chains 269 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 240 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN D 67 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN H 67 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10822 Z= 0.393 Angle : 0.677 10.322 14854 Z= 0.345 Chirality : 0.046 0.156 1594 Planarity : 0.005 0.064 1728 Dihedral : 15.233 172.295 1854 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.81 % Allowed : 32.46 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1130 helix: 1.85 (0.27), residues: 362 sheet: 0.34 (0.28), residues: 326 loop : 0.95 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 89 HIS 0.005 0.001 HIS G 110 PHE 0.012 0.002 PHE B 140 TYR 0.024 0.002 TYR F 29 ARG 0.013 0.001 ARG B 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 1.246 Fit side-chains REVERT: A 57 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7563 (ttm110) REVERT: A 136 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7489 (m110) REVERT: E 88 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: E 104 ASP cc_start: 0.7884 (m-30) cc_final: 0.7679 (m-30) REVERT: G 88 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6995 (pt0) REVERT: I 88 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7077 (tm-30) outliers start: 38 outliers final: 26 residues processed: 282 average time/residue: 1.3100 time to fit residues: 393.5570 Evaluate side-chains 278 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 247 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.0030 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN D 67 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN H 67 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.121072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094108 restraints weight = 17861.570| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.59 r_work: 0.3393 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10822 Z= 0.180 Angle : 0.627 10.139 14854 Z= 0.314 Chirality : 0.042 0.138 1594 Planarity : 0.005 0.061 1728 Dihedral : 15.034 170.301 1850 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.41 % Allowed : 32.97 % Favored : 63.63 % 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: 1.67 (0.26), residues: 1130 helix: 2.03 (0.28), residues: 362 sheet: 0.49 (0.28), residues: 320 loop : 1.01 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 89 HIS 0.005 0.001 HIS C 110 PHE 0.007 0.001 PHE J 69 TYR 0.009 0.001 TYR E 94 ARG 0.014 0.001 ARG B 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6117.09 seconds wall clock time: 107 minutes 33.75 seconds (6453.75 seconds total)