Starting phenix.real_space_refine on Sat Nov 16 06:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/11_2024/8j62_35999.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/11_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_35999/11_2024/8j62_35999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/11_2024/8j62_35999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/11_2024/8j62_35999.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j62_35999/11_2024/8j62_35999.cif" } 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. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10448 Number of models: 1 Model: "" Number of chains: 7 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: "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} 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 Restraints were copied for chains: J, X, H, I, B, G Time building chain proxies: 8.41, per 1000 atoms: 0.80 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 - 3.00 Amino acid : True - 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: 2.39 Conformation dependent library (CDL) restraints added in 1.7 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: 3.82 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: 3.36 Time building geometry restraints manager: 2.85 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: 0.00 - 1.20: 14447 1.20 - 2.40: 304 2.40 - 3.60: 93 3.60 - 4.80: 8 4.80 - 6.00: 2 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 3.040 nonbonded pdb=" OG SER D 53 " pdb=" O6 G X 10 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 112 " pdb=" OP1 U X 8 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 112 " pdb=" OP1 U Y 8 " model vdw 2.227 3.040 nonbonded pdb=" NH2 ARG G 23 " pdb=" OP2 C Y 17 " model vdw 2.239 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 5.990 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 31.880 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.480 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 1.097 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: 1.4454 time to fit residues: 524.2380 Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 261 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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: 0.9980 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 D 45 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10822 Z= 0.263 Angle : 0.568 5.777 14854 Z= 0.301 Chirality : 0.044 0.152 1594 Planarity : 0.004 0.028 1728 Dihedral : 15.130 163.411 1868 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.31 % Allowed : 26.25 % Favored : 68.44 % 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: 1.58 (0.25), residues: 1130 helix: 1.74 (0.26), residues: 374 sheet: 0.53 (0.26), residues: 330 loop : 1.08 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 113 HIS 0.004 0.001 HIS G 43 PHE 0.008 0.001 PHE B 140 TYR 0.017 0.001 TYR J 29 ARG 0.006 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 313 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7543 (ttm110) REVERT: D 28 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8072 (ptmm) REVERT: D 122 MET cc_start: 0.8425 (mmp) cc_final: 0.8170 (mmp) REVERT: E 88 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: G 99 ASP cc_start: 0.7779 (p0) cc_final: 0.7141 (p0) REVERT: H 122 MET cc_start: 0.8395 (mmp) cc_final: 0.8108 (mmp) REVERT: I 88 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7097 (tm-30) outliers start: 53 outliers final: 28 residues processed: 289 average time/residue: 1.4107 time to fit residues: 433.8981 Evaluate side-chains 274 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 95 SER Chi-restraints excluded: chain D residue 28 LYS 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 G residue 107 ILE 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 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: 7.9990 chunk 32 optimal weight: 0.1980 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.8155 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10822 Z= 0.292 Angle : 0.583 6.653 14854 Z= 0.307 Chirality : 0.045 0.168 1594 Planarity : 0.004 0.027 1728 Dihedral : 15.067 166.135 1854 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 6.01 % Allowed : 26.35 % Favored : 67.64 % 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: 1.68 (0.25), residues: 1130 helix: 1.83 (0.26), residues: 374 sheet: 0.62 (0.27), residues: 328 loop : 1.11 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 113 HIS 0.003 0.001 HIS G 73 PHE 0.008 0.001 PHE A 58 TYR 0.011 0.001 TYR G 69 ARG 0.006 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 306 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 246 time to evaluate : 1.163 Fit side-chains REVERT: A 166 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: E 88 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: B 166 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7689 (mp10) outliers start: 60 outliers final: 36 residues processed: 279 average time/residue: 1.5093 time to fit residues: 447.0819 Evaluate side-chains 278 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 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 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 53 SER 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 118 ARG Chi-restraints excluded: chain D residue 125 LEU 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 F residue 108 VAL 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 166 GLN 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 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 85 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 108 VAL 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: 0.9980 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** F 41 GLN B 96 GLN ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10822 Z= 0.229 Angle : 0.581 9.433 14854 Z= 0.301 Chirality : 0.043 0.159 1594 Planarity : 0.004 0.027 1728 Dihedral : 15.048 166.195 1854 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.31 % Allowed : 27.35 % Favored : 67.33 % 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: 1.73 (0.25), residues: 1130 helix: 1.94 (0.26), residues: 376 sheet: 0.67 (0.27), residues: 328 loop : 1.03 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 89 HIS 0.003 0.001 HIS G 56 PHE 0.007 0.001 PHE A 58 TYR 0.020 0.001 TYR F 29 ARG 0.008 0.001 ARG D 49 *********************** 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 306 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 1.359 Fit side-chains REVERT: A 57 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7571 (ttm110) REVERT: A 166 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: B 166 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: G 88 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6952 (pt0) outliers start: 53 outliers final: 29 residues processed: 284 average time/residue: 1.5565 time to fit residues: 469.7074 Evaluate side-chains 267 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 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 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 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 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 107 ILE 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: 3.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** F 37 HIS F 41 GLN B 96 GLN H 45 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: 0.8134 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10822 Z= 0.214 Angle : 0.588 9.799 14854 Z= 0.300 Chirality : 0.043 0.167 1594 Planarity : 0.004 0.037 1728 Dihedral : 15.025 165.584 1854 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.51 % Allowed : 27.76 % Favored : 66.73 % 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: 1.78 (0.25), residues: 1130 helix: 2.05 (0.26), residues: 376 sheet: 0.72 (0.27), residues: 324 loop : 0.94 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 89 HIS 0.003 0.001 HIS C 28 PHE 0.007 0.001 PHE J 69 TYR 0.010 0.001 TYR G 69 ARG 0.008 0.001 ARG G 23 *********************** 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 297 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 1.285 Fit side-chains REVERT: A 57 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7553 (ttm110) REVERT: A 166 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: E 17 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (ttp-170) REVERT: B 166 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: G 88 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6941 (pt0) REVERT: G 91 LYS cc_start: 0.8564 (tppp) cc_final: 0.8347 (tppt) outliers start: 55 outliers final: 34 residues processed: 277 average time/residue: 1.4898 time to fit residues: 438.5926 Evaluate side-chains 273 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 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 107 ILE 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: 7.9990 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 108 optimal weight: 0.1980 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN D 41 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 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: 0.8150 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10822 Z= 0.247 Angle : 0.599 10.198 14854 Z= 0.308 Chirality : 0.044 0.146 1594 Planarity : 0.004 0.048 1728 Dihedral : 15.040 165.972 1854 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.91 % Allowed : 27.66 % Favored : 66.43 % 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: 1.78 (0.25), residues: 1130 helix: 2.06 (0.26), residues: 376 sheet: 0.73 (0.28), residues: 324 loop : 0.93 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 89 HIS 0.007 0.001 HIS C 110 PHE 0.007 0.001 PHE H 68 TYR 0.022 0.001 TYR J 29 ARG 0.011 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 304 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 1.029 Fit side-chains REVERT: A 57 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7557 (ttm110) REVERT: A 166 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: B 166 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: G 88 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6941 (pt0) REVERT: I 17 ARG cc_start: 0.8092 (ttp-170) cc_final: 0.7879 (mtp85) REVERT: I 97 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7554 (mp10) outliers start: 59 outliers final: 39 residues processed: 280 average time/residue: 1.4841 time to fit residues: 440.9418 Evaluate side-chains 282 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 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 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 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 97 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 58 VAL 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: 1.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 G 110 HIS ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10822 Z= 0.272 Angle : 0.628 9.674 14854 Z= 0.321 Chirality : 0.044 0.148 1594 Planarity : 0.004 0.048 1728 Dihedral : 15.073 166.609 1854 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.71 % Allowed : 29.26 % Favored : 65.03 % 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: 1.68 (0.25), residues: 1130 helix: 1.91 (0.27), residues: 376 sheet: 0.73 (0.28), residues: 324 loop : 0.89 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 89 HIS 0.007 0.001 HIS C 110 PHE 0.007 0.001 PHE H 68 TYR 0.010 0.001 TYR C 69 ARG 0.011 0.001 ARG A 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 to be fit. rotamer outliers: 57 poor density : 237 time to evaluate : 1.337 Fit side-chains REVERT: A 57 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7558 (ttm110) REVERT: A 166 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: C 88 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6959 (pt0) REVERT: E 97 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: B 166 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7608 (mp10) REVERT: G 88 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6944 (pt0) REVERT: I 17 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7526 (ttm170) REVERT: I 171 GLU cc_start: 0.8217 (pp20) cc_final: 0.7962 (pm20) outliers start: 57 outliers final: 40 residues processed: 273 average time/residue: 1.4586 time to fit residues: 423.0627 Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU 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 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 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 53 SER 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 17 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 58 VAL 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: 6.9990 chunk 21 optimal weight: 0.0970 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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** ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10822 Z= 0.232 Angle : 0.630 9.168 14854 Z= 0.321 Chirality : 0.044 0.143 1594 Planarity : 0.004 0.058 1728 Dihedral : 15.036 166.102 1852 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.21 % Allowed : 29.86 % Favored : 64.93 % 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: 1.70 (0.25), residues: 1130 helix: 1.95 (0.27), residues: 376 sheet: 0.72 (0.28), residues: 324 loop : 0.90 (0.32), residues: 430 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 0.007 0.001 PHE A 58 TYR 0.021 0.001 TYR J 29 ARG 0.014 0.001 ARG B 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 300 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 1.138 Fit side-chains REVERT: A 57 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7522 (ttm110) REVERT: A 66 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8770 (mttp) REVERT: A 166 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: C 88 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6948 (pt0) REVERT: E 17 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7726 (ttt180) REVERT: E 97 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: E 171 GLU cc_start: 0.8201 (pm20) cc_final: 0.7827 (pm20) REVERT: B 166 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: G 88 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6938 (pt0) REVERT: I 17 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7549 (ttm170) outliers start: 52 outliers final: 38 residues processed: 280 average time/residue: 1.4774 time to fit residues: 439.1577 Evaluate side-chains 282 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 66 LYS 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 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU 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 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 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 17 ARG Chi-restraints excluded: chain I residue 107 ILE 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: 7.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10822 Z= 0.278 Angle : 0.651 9.521 14854 Z= 0.333 Chirality : 0.044 0.149 1594 Planarity : 0.005 0.063 1728 Dihedral : 15.087 167.234 1852 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 5.31 % Allowed : 29.76 % Favored : 64.93 % 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: 1.64 (0.25), residues: 1130 helix: 1.92 (0.27), residues: 364 sheet: 0.71 (0.28), residues: 320 loop : 0.85 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 89 HIS 0.007 0.001 HIS G 110 PHE 0.009 0.001 PHE F 69 TYR 0.010 0.001 TYR H 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 289 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7540 (ttm110) REVERT: A 66 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8739 (mttp) REVERT: A 166 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: C 88 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6949 (pt0) REVERT: E 97 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7571 (mp10) REVERT: B 166 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: G 88 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6937 (pt0) outliers start: 53 outliers final: 40 residues processed: 269 average time/residue: 1.5319 time to fit residues: 437.8528 Evaluate side-chains 280 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 66 LYS 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 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU 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 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 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 107 ILE 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: 0.8980 chunk 115 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 41 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: 0.8181 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10822 Z= 0.339 Angle : 0.697 9.741 14854 Z= 0.357 Chirality : 0.046 0.148 1594 Planarity : 0.005 0.065 1728 Dihedral : 15.176 169.473 1852 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.81 % Allowed : 30.16 % Favored : 65.03 % 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: 1.48 (0.25), residues: 1130 helix: 1.77 (0.27), residues: 364 sheet: 0.54 (0.28), residues: 324 loop : 0.87 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 89 HIS 0.006 0.001 HIS G 110 PHE 0.009 0.001 PHE F 69 TYR 0.022 0.001 TYR F 29 ARG 0.013 0.001 ARG A 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 282 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 1.089 Fit side-chains REVERT: A 57 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7606 (ttm110) REVERT: A 66 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8737 (mttp) REVERT: A 166 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: C 88 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6953 (pt0) REVERT: E 97 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: B 166 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: G 88 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6956 (pt0) outliers start: 48 outliers final: 36 residues processed: 267 average time/residue: 1.1506 time to fit residues: 327.4000 Evaluate side-chains 275 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 66 LYS 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 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU 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 54 GLU 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 15 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 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 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 107 ILE 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: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.119537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091999 restraints weight = 17851.450| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.60 r_work: 0.3356 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10822 Z= 0.239 Angle : 0.660 9.570 14854 Z= 0.338 Chirality : 0.044 0.139 1594 Planarity : 0.005 0.063 1728 Dihedral : 15.095 168.657 1850 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.61 % Allowed : 31.16 % 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: 1.54 (0.26), residues: 1130 helix: 1.85 (0.28), residues: 364 sheet: 0.58 (0.28), residues: 322 loop : 0.86 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 89 HIS 0.006 0.001 HIS G 110 PHE 0.007 0.001 PHE D 44 TYR 0.010 0.001 TYR G 69 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: 6393.19 seconds wall clock time: 115 minutes 0.68 seconds (6900.68 seconds total)