Starting phenix.real_space_refine on Mon Mar 18 02:03:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8x_16494/03_2024/8c8x_16494.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8x_16494/03_2024/8c8x_16494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8x_16494/03_2024/8c8x_16494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8x_16494/03_2024/8c8x_16494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8x_16494/03_2024/8c8x_16494.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8x_16494/03_2024/8c8x_16494.pdb" } resolution = 3.93 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= 0.003 sd= 0.107 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: 5 Type Number sf(0) Gaussians P 2823 5.49 5 S 66 5.16 5 C 40942 2.51 5 N 15445 2.21 5 O 23500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T GLU 4": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 82776 Number of models: 1 Model: "" Number of chains: 28 Chain: "C" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1858 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 13, 'TRANS': 227} Chain breaks: 1 Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1393 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "E" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1462 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 499 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 984 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain breaks: 1 Chain: "A" Number of atoms: 58086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2705, 58086 Classifications: {'RNA': 2705} Modifications used: {'rna2p_pur': 262, 'rna2p_pyr': 151, 'rna3p_pur': 1304, 'rna3p_pyr': 988} Link IDs: {'rna2p': 412, 'rna3p': 2292} Chain breaks: 3 Chain: "B" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2546 Classifications: {'RNA': 119} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Residues with excluded nonbonded symmetry interactions: 100 residue: pdb=" P C A 840 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C A 840 " occ=0.00 residue: pdb=" P G A 841 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G A 841 " occ=0.00 residue: pdb=" P U A 842 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 842 " occ=0.00 residue: pdb=" P G A 843 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G A 843 " occ=0.00 residue: pdb=" P A A 844 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A A 844 " occ=0.00 residue: pdb=" P A A 845 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A A 845 " occ=0.00 residue: pdb=" P U A 846 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 846 " occ=0.00 residue: pdb=" P U A 847 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 847 " occ=0.00 residue: pdb=" P C A 848 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C A 848 " occ=0.00 residue: pdb=" P A A 849 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A A 849 " occ=0.00 residue: pdb=" P U A 850 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 850 " occ=0.00 residue: pdb=" P C A 851 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C A 851 " occ=0.00 ... (remaining 88 not shown) Time building chain proxies: 32.58, per 1000 atoms: 0.39 Number of scatterers: 82776 At special positions: 0 Unit cell: (195, 232.5, 216.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 2823 15.00 O 23500 8.00 N 15445 7.00 C 40942 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: 37.39 Conformation dependent library (CDL) restraints added in 3.5 seconds 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5178 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 38 sheets defined 30.5% alpha, 19.7% beta 903 base pairs and 1389 stacking pairs defined. Time for finding SS restraints: 30.68 Creating SS restraints... Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.163A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.647A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.167A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.581A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.544A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 20 removed outlier: 3.664A pdb=" N GLU F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.922A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.539A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 134 through 137 Processing helix chain 'F' and resid 161 through 170 Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 43 through 48 Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.341A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 122 Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.591A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 112 Processing helix chain 'K' and resid 113 through 118 removed outlier: 3.706A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 113 through 118' Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'L' and resid 127 through 138 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.794A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 88 Processing helix chain 'O' and resid 2 through 20 removed outlier: 3.654A pdb=" N ARG O 6 " --> pdb=" O LYS O 2 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG O 12 " --> pdb=" O ARG O 8 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU O 20 " --> pdb=" O LYS O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 59 Processing helix chain 'O' and resid 66 through 85 Processing helix chain 'O' and resid 100 through 114 removed outlier: 3.589A pdb=" N GLY O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 12 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 97 through 102 removed outlier: 4.108A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 107 removed outlier: 3.510A pdb=" N ALA P 106 " --> pdb=" O THR P 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 20 Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.009A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.681A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 4.172A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.798A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 5 through 10 Processing helix chain 'T' and resid 17 through 28 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'V' and resid 13 through 23 Processing helix chain 'V' and resid 44 through 51 removed outlier: 3.984A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 58 removed outlier: 6.476A pdb=" N GLU V 55 " --> pdb=" O ALA V 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 62 removed outlier: 4.911A pdb=" N LYS X 60 " --> pdb=" O ARG X 56 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 2 through 7 removed outlier: 3.903A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 24 through 34 Processing helix chain 'Y' and resid 39 through 42 removed outlier: 3.502A pdb=" N LEU Y 42 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 39 through 42' Processing helix chain 'Y' and resid 43 through 56 removed outlier: 3.887A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP Y 49 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing helix chain '0' and resid 8 through 18 removed outlier: 3.947A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.067A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 36 through 43 Processing helix chain '3' and resid 50 through 52 No H-bonds generated for 'chain '3' and resid 50 through 52' Processing helix chain '3' and resid 53 through 61 Processing helix chain 'M' and resid 43 through 54 removed outlier: 3.561A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 124 removed outlier: 3.671A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.608A pdb=" N GLU C 34 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.523A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.737A pdb=" N THR C 190 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS C 141 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.978A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 169 through 171 removed outlier: 4.787A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 14 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 22 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.027A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 117 through 118 removed outlier: 4.172A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET D 165 " --> pdb=" O GLY D 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.272A pdb=" N LEU E 147 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR E 189 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE E 149 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 65 through 68 removed outlier: 3.931A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 19 through 20 removed outlier: 4.038A pdb=" N VAL H 19 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL H 3 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 123 through 124 removed outlier: 6.175A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU J 140 " --> pdb=" O TRP J 15 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL J 17 " --> pdb=" O LEU J 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.934A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL K 62 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL K 85 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.956A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY P 44 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER P 84 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS P 28 " --> pdb=" O SER P 82 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 73 through 75 Processing sheet with id=AB7, first strand: chain 'L' and resid 88 through 89 removed outlier: 6.284A pdb=" N VAL L 89 " --> pdb=" O ARG L 122 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL L 121 " --> pdb=" O GLU L 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'O' and resid 46 through 51 removed outlier: 4.091A pdb=" N VAL O 48 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG O 24 " --> pdb=" O ILE O 39 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU O 25 " --> pdb=" O ASP O 92 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.578A pdb=" N ALA R 42 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL R 4 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 19 through 22 removed outlier: 7.363A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL R 64 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR R 99 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.988A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.372A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP S 94 " --> pdb=" O ARG S 84 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG S 84 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE S 96 " --> pdb=" O MET S 82 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET S 82 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LYS S 98 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR S 100 " --> pdb=" O GLU S 78 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU S 78 " --> pdb=" O THR S 100 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR S 104 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.773A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 63 through 65 removed outlier: 6.450A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE U 72 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 40 through 43 removed outlier: 3.655A pdb=" N VAL U 41 " --> pdb=" O LYS U 60 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL U 58 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 82 through 85 removed outlier: 4.548A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 3 through 7 removed outlier: 7.867A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU V 42 " --> pdb=" O PHE V 26 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN V 78 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE V 89 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP V 76 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE V 91 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA V 74 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG V 93 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL V 72 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 13 through 14 removed outlier: 6.679A pdb=" N ILE W 27 " --> pdb=" O ALA W 52 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA W 52 " --> pdb=" O ILE W 27 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL W 29 " --> pdb=" O LEU W 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY W 43 " --> pdb=" O PHE W 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 21 through 22 Processing sheet with id=AD3, first strand: chain 'X' and resid 12 through 15 removed outlier: 3.789A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 32 through 38 Processing sheet with id=AD5, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AD6, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AD7, first strand: chain '0' and resid 47 through 48 removed outlier: 3.640A pdb=" N TYR 0 48 " --> pdb=" O ARG 0 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '1' and resid 17 through 22 removed outlier: 3.672A pdb=" N VAL 1 9 " --> pdb=" O LYS 1 47 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN 1 42 " --> pdb=" O ASP 1 37 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS 1 35 " --> pdb=" O VAL 1 44 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU 1 33 " --> pdb=" O TYR 1 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '3' and resid 14 through 15 removed outlier: 3.942A pdb=" N LYS 3 14 " --> pdb=" O LYS 3 22 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 3 22 " --> pdb=" O LYS 3 14 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA 3 47 " --> pdb=" O HIS 3 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.868A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP M 106 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 39 through 42 removed outlier: 4.148A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE M 96 " --> pdb=" O GLY M 39 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 2112 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2289 hydrogen bonds 3620 hydrogen bond angles 0 basepair planarities 903 basepair parallelities 1389 stacking parallelities Total time for adding SS restraints: 122.94 Time building geometry restraints manager: 40.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 28616 1.38 - 1.54: 55907 1.54 - 1.71: 5688 1.71 - 1.87: 126 1.87 - 2.04: 1 Bond restraints: 90338 Sorted by residual: bond pdb=" C1' G A2722 " pdb=" N9 G A2722 " ideal model delta sigma weight residual 1.475 2.040 -0.565 1.50e-02 4.44e+03 1.42e+03 bond pdb=" C6 A A2721 " pdb=" N1 A A2721 " ideal model delta sigma weight residual 1.351 1.814 -0.463 2.00e-02 2.50e+03 5.35e+02 bond pdb=" N1 A A2721 " pdb=" C2 A A2721 " ideal model delta sigma weight residual 1.339 1.728 -0.389 2.00e-02 2.50e+03 3.79e+02 bond pdb=" N3 A A2721 " pdb=" C4 A A2721 " ideal model delta sigma weight residual 1.344 1.713 -0.369 2.00e-02 2.50e+03 3.41e+02 bond pdb=" C2 A A2721 " pdb=" N3 A A2721 " ideal model delta sigma weight residual 1.331 1.690 -0.359 2.00e-02 2.50e+03 3.22e+02 ... (remaining 90333 not shown) Histogram of bond angle deviations from ideal: 76.80 - 89.82: 1 89.82 - 102.84: 5336 102.84 - 115.86: 73638 115.86 - 128.88: 54347 128.88 - 141.90: 2638 Bond angle restraints: 135960 Sorted by residual: angle pdb=" C2' G A2722 " pdb=" C1' G A2722 " pdb=" N9 G A2722 " ideal model delta sigma weight residual 112.00 126.90 -14.90 1.50e+00 4.44e-01 9.87e+01 angle pdb=" C8 G A2722 " pdb=" N9 G A2722 " pdb=" C4 G A2722 " ideal model delta sigma weight residual 106.40 76.80 29.60 3.00e+00 1.11e-01 9.74e+01 angle pdb=" O4' G A2722 " pdb=" C1' G A2722 " pdb=" N9 G A2722 " ideal model delta sigma weight residual 108.50 118.82 -10.32 1.50e+00 4.44e-01 4.73e+01 angle pdb=" N9 G A2722 " pdb=" C8 G A2722 " pdb=" N7 G A2722 " ideal model delta sigma weight residual 113.10 132.67 -19.57 3.00e+00 1.11e-01 4.26e+01 angle pdb=" C1' G A2722 " pdb=" N9 G A2722 " pdb=" C4 G A2722 " ideal model delta sigma weight residual 126.50 141.90 -15.40 3.00e+00 1.11e-01 2.63e+01 ... (remaining 135955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 51004 35.93 - 71.86: 6137 71.86 - 107.78: 749 107.78 - 143.71: 18 143.71 - 179.64: 15 Dihedral angle restraints: 57923 sinusoidal: 49891 harmonic: 8032 Sorted by residual: dihedral pdb=" O4' U A2473 " pdb=" C1' U A2473 " pdb=" N1 U A2473 " pdb=" C2 U A2473 " ideal model delta sinusoidal sigma weight residual 200.00 42.01 157.99 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 50.42 149.58 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' U A1584 " pdb=" C1' U A1584 " pdb=" N1 U A1584 " pdb=" C2 U A1584 " ideal model delta sinusoidal sigma weight residual 200.00 52.47 147.53 1 1.50e+01 4.44e-03 7.87e+01 ... (remaining 57920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 17107 0.078 - 0.157: 378 0.157 - 0.235: 1 0.235 - 0.314: 0 0.314 - 0.392: 1 Chirality restraints: 17487 Sorted by residual: chirality pdb=" C1' G A2722 " pdb=" O4' G A2722 " pdb=" C2' G A2722 " pdb=" N9 G A2722 " both_signs ideal model delta sigma weight residual False 2.46 2.07 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA ILE T 2 " pdb=" N ILE T 2 " pdb=" C ILE T 2 " pdb=" CB ILE T 2 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" C2' G A2722 " pdb=" C3' G A2722 " pdb=" O2' G A2722 " pdb=" C1' G A2722 " both_signs ideal model delta sigma weight residual False -2.75 -2.90 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 17484 not shown) Planarity restraints: 6684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A2721 " -0.032 2.00e-02 2.50e+03 2.23e-02 1.36e+01 pdb=" N9 A A2721 " 0.037 2.00e-02 2.50e+03 pdb=" C8 A A2721 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A A2721 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A2721 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A2721 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A A2721 " 0.001 2.00e-02 2.50e+03 pdb=" N1 A A2721 " -0.029 2.00e-02 2.50e+03 pdb=" C2 A A2721 " 0.042 2.00e-02 2.50e+03 pdb=" N3 A A2721 " -0.018 2.00e-02 2.50e+03 pdb=" C4 A A2721 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.014 2.00e-02 2.50e+03 1.74e-02 9.06e+00 pdb=" N9 G A 259 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 259 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G A 259 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.045 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.033 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 259 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1727 " -0.010 2.00e-02 2.50e+03 1.98e-02 8.83e+00 pdb=" N1 C A1727 " 0.002 2.00e-02 2.50e+03 pdb=" C2 C A1727 " 0.049 2.00e-02 2.50e+03 pdb=" O2 C A1727 " -0.026 2.00e-02 2.50e+03 pdb=" N3 C A1727 " -0.007 2.00e-02 2.50e+03 pdb=" C4 C A1727 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C A1727 " -0.012 2.00e-02 2.50e+03 pdb=" C5 C A1727 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A1727 " -0.001 2.00e-02 2.50e+03 ... (remaining 6681 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 305 2.33 - 2.97: 37792 2.97 - 3.62: 138939 3.62 - 4.26: 234673 4.26 - 4.90: 319874 Nonbonded interactions: 731583 Sorted by model distance: nonbonded pdb=" N1 A A2721 " pdb=" N9 G A2722 " model vdw 1.690 3.200 nonbonded pdb=" C2 A A2721 " pdb=" N9 G A2722 " model vdw 1.813 3.420 nonbonded pdb=" C6 A A2721 " pdb=" N9 G A2722 " model vdw 1.884 3.340 nonbonded pdb=" N3 A A2721 " pdb=" N9 G A2722 " model vdw 1.918 3.200 nonbonded pdb=" N1 A A2721 " pdb=" C1' G A2722 " model vdw 1.919 3.550 ... (remaining 731578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 9.080 Check model and map are aligned: 0.940 Set scattering table: 0.590 Process input model: 283.480 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 299.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 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 : 0.004 0.565 90338 Z= 0.245 Angle : 0.396 29.603 135960 Z= 0.200 Chirality : 0.026 0.392 17487 Planarity : 0.002 0.034 6684 Dihedral : 22.690 179.641 52745 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 0.30 % Allowed : 2.65 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2772 helix: 2.06 (0.21), residues: 758 sheet: -0.13 (0.24), residues: 470 loop : -0.49 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 212 HIS 0.003 0.000 HIS V 80 PHE 0.007 0.001 PHE M 130 TYR 0.006 0.001 TYR N 112 ARG 0.003 0.000 ARG W 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 676 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7796 (tm-30) REVERT: D 84 LEU cc_start: 0.8733 (mm) cc_final: 0.8434 (mm) REVERT: D 175 LEU cc_start: 0.8745 (tt) cc_final: 0.8530 (tt) REVERT: D 200 ASP cc_start: 0.8225 (m-30) cc_final: 0.7896 (m-30) REVERT: F 16 MET cc_start: 0.7520 (mmm) cc_final: 0.7296 (mmm) REVERT: F 80 GLN cc_start: 0.9106 (tp40) cc_final: 0.8709 (tp40) REVERT: F 133 GLU cc_start: 0.8162 (mp0) cc_final: 0.7481 (mp0) REVERT: H 35 LYS cc_start: 0.6966 (ttmm) cc_final: 0.6461 (pptt) REVERT: J 49 ASP cc_start: 0.8312 (p0) cc_final: 0.7812 (p0) REVERT: J 67 ASN cc_start: 0.6800 (t0) cc_final: 0.6174 (t0) REVERT: J 106 LYS cc_start: 0.9343 (tptt) cc_final: 0.9109 (tptt) REVERT: K 9 ASN cc_start: 0.8539 (t0) cc_final: 0.8166 (m-40) REVERT: O 89 VAL cc_start: 0.8319 (m) cc_final: 0.8117 (m) REVERT: O 91 PHE cc_start: 0.7651 (t80) cc_final: 0.7143 (t80) REVERT: Q 58 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7425 (mm-40) REVERT: Q 80 ASN cc_start: 0.9005 (t0) cc_final: 0.8566 (m-40) REVERT: R 26 ASP cc_start: 0.8352 (t0) cc_final: 0.8040 (t0) REVERT: S 12 SER cc_start: 0.9128 (t) cc_final: 0.8897 (t) REVERT: S 68 ASP cc_start: 0.7934 (t0) cc_final: 0.7546 (t0) REVERT: T 29 THR cc_start: 0.8100 (m) cc_final: 0.7712 (p) REVERT: T 56 GLU cc_start: 0.8227 (tp30) cc_final: 0.7754 (mm-30) REVERT: T 77 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8302 (mmt90) REVERT: U 52 ASN cc_start: 0.4140 (t0) cc_final: 0.3939 (t0) REVERT: V 59 GLU cc_start: 0.4030 (pt0) cc_final: 0.3312 (pt0) REVERT: V 70 ILE cc_start: 0.8124 (tp) cc_final: 0.7865 (tt) REVERT: W 5 ARG cc_start: 0.5424 (ptt90) cc_final: 0.4330 (ptt-90) REVERT: W 8 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6209 (tm-30) REVERT: W 10 LYS cc_start: 0.7421 (tttm) cc_final: 0.6126 (mppt) REVERT: W 69 LYS cc_start: 0.7253 (tptt) cc_final: 0.7048 (tptm) REVERT: Y 36 GLN cc_start: 0.8114 (pt0) cc_final: 0.7773 (pm20) REVERT: Y 49 ASP cc_start: 0.7755 (p0) cc_final: 0.7533 (p0) REVERT: 0 41 HIS cc_start: 0.6622 (m90) cc_final: 0.6196 (m90) REVERT: 1 37 ASP cc_start: 0.7079 (t0) cc_final: 0.6187 (p0) REVERT: 1 40 VAL cc_start: 0.6914 (p) cc_final: 0.6140 (t) REVERT: 3 60 CYS cc_start: 0.9025 (m) cc_final: 0.8738 (m) REVERT: 3 63 TYR cc_start: 0.6796 (m-10) cc_final: 0.6311 (m-10) REVERT: M 124 LEU cc_start: 0.8205 (tp) cc_final: 0.7888 (tp) outliers start: 7 outliers final: 0 residues processed: 679 average time/residue: 0.7969 time to fit residues: 914.6251 Evaluate side-chains 400 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 468 optimal weight: 20.0000 chunk 420 optimal weight: 30.0000 chunk 233 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 283 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 435 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 264 optimal weight: 50.0000 chunk 323 optimal weight: 10.0000 chunk 504 optimal weight: 20.0000 overall best weight: 10.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 46 GLN E 90 GLN F 26 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS O 37 GLN P 2 ASN P 65 ASN R 86 GLN S 31 GLN T 59 ASN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN X 22 ASN ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.566 90338 Z= 0.514 Angle : 0.842 38.123 135960 Z= 0.409 Chirality : 0.040 0.389 17487 Planarity : 0.007 0.110 6684 Dihedral : 23.762 179.954 47159 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.47 % Favored : 92.50 % Rotamer: Outliers : 3.69 % Allowed : 13.24 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2772 helix: 0.48 (0.18), residues: 742 sheet: -0.58 (0.21), residues: 564 loop : -1.01 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP X 38 HIS 0.017 0.003 HIS C 199 PHE 0.045 0.003 PHE F 99 TYR 0.034 0.003 TYR F 6 ARG 0.022 0.001 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 428 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8952 (mm-30) REVERT: C 180 MET cc_start: 0.7952 (pmm) cc_final: 0.7713 (pmm) REVERT: D 200 ASP cc_start: 0.8242 (m-30) cc_final: 0.8013 (m-30) REVERT: E 176 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8049 (p0) REVERT: F 80 GLN cc_start: 0.8992 (tp40) cc_final: 0.8745 (tp40) REVERT: F 111 ARG cc_start: 0.5905 (mtm-85) cc_final: 0.5382 (ptm-80) REVERT: F 133 GLU cc_start: 0.8247 (mp0) cc_final: 0.7609 (mp0) REVERT: H 33 GLN cc_start: 0.6068 (OUTLIER) cc_final: 0.5839 (pm20) REVERT: J 9 GLU cc_start: 0.8592 (pm20) cc_final: 0.8357 (pm20) REVERT: J 49 ASP cc_start: 0.8430 (p0) cc_final: 0.7860 (p0) REVERT: J 67 ASN cc_start: 0.6936 (t0) cc_final: 0.6684 (t0) REVERT: K 7 MET cc_start: 0.8431 (tpp) cc_final: 0.8231 (tpp) REVERT: K 9 ASN cc_start: 0.8923 (t0) cc_final: 0.8528 (t0) REVERT: N 72 ASP cc_start: 0.8486 (m-30) cc_final: 0.8230 (m-30) REVERT: O 91 PHE cc_start: 0.7796 (t80) cc_final: 0.7431 (t80) REVERT: P 2 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8535 (m-40) REVERT: P 10 GLU cc_start: 0.9147 (pt0) cc_final: 0.8920 (pt0) REVERT: P 28 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7529 (mtpp) REVERT: Q 35 PHE cc_start: 0.9500 (t80) cc_final: 0.9138 (t80) REVERT: Q 39 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8671 (tp) REVERT: Q 48 ASP cc_start: 0.8562 (m-30) cc_final: 0.8318 (m-30) REVERT: R 26 ASP cc_start: 0.8566 (t0) cc_final: 0.8241 (t0) REVERT: S 68 ASP cc_start: 0.8548 (t0) cc_final: 0.8131 (t0) REVERT: T 56 GLU cc_start: 0.8327 (tp30) cc_final: 0.7624 (mm-30) REVERT: T 77 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.8304 (mmt90) REVERT: V 51 GLN cc_start: 0.7270 (mt0) cc_final: 0.6838 (mt0) REVERT: V 59 GLU cc_start: 0.4087 (pt0) cc_final: 0.3725 (pt0) REVERT: W 5 ARG cc_start: 0.5844 (ptt90) cc_final: 0.4541 (mpp80) REVERT: W 8 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6906 (tm-30) REVERT: W 41 ASN cc_start: 0.8573 (t0) cc_final: 0.8186 (t0) REVERT: W 73 ILE cc_start: 0.8883 (tt) cc_final: 0.8584 (tt) REVERT: X 51 SER cc_start: 0.9219 (t) cc_final: 0.8805 (p) REVERT: X 77 TYR cc_start: 0.8416 (p90) cc_final: 0.8207 (p90) REVERT: Y 1 MET cc_start: 0.8267 (ppp) cc_final: 0.7818 (ppp) REVERT: Y 13 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8051 (mt-10) REVERT: Y 30 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8912 (mmp) REVERT: Y 60 LYS cc_start: 0.8014 (pptt) cc_final: 0.7656 (pttp) REVERT: 0 5 ASN cc_start: 0.9081 (m110) cc_final: 0.8797 (m110) REVERT: 1 6 ILE cc_start: 0.7621 (pt) cc_final: 0.7293 (pt) REVERT: 1 37 ASP cc_start: 0.7152 (t0) cc_final: 0.6392 (p0) REVERT: 1 40 VAL cc_start: 0.7328 (p) cc_final: 0.6588 (t) REVERT: 3 60 CYS cc_start: 0.9252 (m) cc_final: 0.8935 (m) REVERT: M 104 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7346 (mt-10) outliers start: 85 outliers final: 59 residues processed: 480 average time/residue: 0.7920 time to fit residues: 657.3785 Evaluate side-chains 427 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 363 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 34 HIS Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain M residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 280 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 419 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 504 optimal weight: 20.0000 chunk 545 optimal weight: 20.0000 chunk 449 optimal weight: 10.0000 chunk 500 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 86 GLN T 48 GLN T 70 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 16 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.572 90338 Z= 0.416 Angle : 0.674 36.963 135960 Z= 0.333 Chirality : 0.035 0.485 17487 Planarity : 0.005 0.082 6684 Dihedral : 23.806 176.959 47159 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.26 % Allowed : 16.02 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 2772 helix: 0.50 (0.19), residues: 744 sheet: -0.72 (0.21), residues: 547 loop : -1.18 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 96 HIS 0.015 0.002 HIS 0 41 PHE 0.024 0.002 PHE R 53 TYR 0.034 0.003 TYR F 7 ARG 0.014 0.001 ARG W 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 413 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 GLU cc_start: 0.8871 (tp30) cc_final: 0.8638 (mp0) REVERT: D 11 MET cc_start: 0.7903 (ppp) cc_final: 0.7493 (ptm) REVERT: D 156 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: D 173 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7759 (mm-40) REVERT: D 175 LEU cc_start: 0.8845 (tt) cc_final: 0.8644 (tt) REVERT: D 200 ASP cc_start: 0.8197 (m-30) cc_final: 0.7863 (m-30) REVERT: E 150 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8165 (p) REVERT: E 176 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7961 (p0) REVERT: F 77 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7909 (mmtt) REVERT: F 133 GLU cc_start: 0.8371 (mp0) cc_final: 0.7718 (mp0) REVERT: J 49 ASP cc_start: 0.8558 (p0) cc_final: 0.7868 (p0) REVERT: J 67 ASN cc_start: 0.6933 (t0) cc_final: 0.6686 (t0) REVERT: J 114 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9157 (mm) REVERT: K 9 ASN cc_start: 0.8846 (t0) cc_final: 0.8482 (t0) REVERT: K 20 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7341 (tpt) REVERT: O 91 PHE cc_start: 0.8018 (t80) cc_final: 0.7650 (t80) REVERT: Q 19 GLN cc_start: 0.8460 (mp10) cc_final: 0.8147 (mp10) REVERT: Q 35 PHE cc_start: 0.9480 (t80) cc_final: 0.9150 (t80) REVERT: Q 39 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8687 (tp) REVERT: Q 48 ASP cc_start: 0.8426 (m-30) cc_final: 0.8195 (m-30) REVERT: Q 58 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8121 (mm-40) REVERT: Q 93 ILE cc_start: 0.9407 (mm) cc_final: 0.9179 (mt) REVERT: R 81 LYS cc_start: 0.8949 (mmtp) cc_final: 0.8725 (mmtp) REVERT: S 68 ASP cc_start: 0.8422 (t0) cc_final: 0.8125 (t0) REVERT: T 24 MET cc_start: 0.7909 (tpp) cc_final: 0.7510 (tpp) REVERT: T 56 GLU cc_start: 0.8156 (tp30) cc_final: 0.7526 (mm-30) REVERT: T 77 ARG cc_start: 0.8735 (mtt-85) cc_final: 0.8326 (mmt90) REVERT: W 5 ARG cc_start: 0.6044 (ptt90) cc_final: 0.4638 (mpp80) REVERT: W 12 LEU cc_start: 0.8583 (mm) cc_final: 0.8374 (mm) REVERT: X 29 LEU cc_start: 0.9337 (mm) cc_final: 0.9065 (mm) REVERT: X 51 SER cc_start: 0.9274 (t) cc_final: 0.8848 (p) REVERT: X 77 TYR cc_start: 0.8363 (p90) cc_final: 0.8091 (p90) REVERT: Y 1 MET cc_start: 0.8106 (ppp) cc_final: 0.7521 (ppp) REVERT: Y 13 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8084 (mt-10) REVERT: Y 25 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7993 (tp40) REVERT: Y 30 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8919 (mmp) REVERT: 0 11 LYS cc_start: 0.8724 (tptp) cc_final: 0.8445 (tptp) REVERT: 0 15 ARG cc_start: 0.9245 (ttp80) cc_final: 0.8697 (ttp80) REVERT: 1 37 ASP cc_start: 0.7422 (t0) cc_final: 0.6475 (p0) REVERT: 1 40 VAL cc_start: 0.7486 (p) cc_final: 0.6803 (t) REVERT: 3 60 CYS cc_start: 0.9324 (m) cc_final: 0.9023 (m) outliers start: 98 outliers final: 67 residues processed: 461 average time/residue: 0.8634 time to fit residues: 698.1765 Evaluate side-chains 445 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 370 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 498 optimal weight: 20.0000 chunk 379 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 339 optimal weight: 20.0000 chunk 506 optimal weight: 20.0000 chunk 536 optimal weight: 10.0000 chunk 264 optimal weight: 40.0000 chunk 480 optimal weight: 50.0000 chunk 144 optimal weight: 30.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.571 90338 Z= 0.493 Angle : 0.813 37.405 135960 Z= 0.403 Chirality : 0.041 0.439 17487 Planarity : 0.006 0.083 6684 Dihedral : 24.103 179.155 47159 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 29.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.49 % Favored : 90.40 % Rotamer: Outliers : 6.43 % Allowed : 16.85 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.15), residues: 2772 helix: -0.03 (0.18), residues: 764 sheet: -1.08 (0.21), residues: 538 loop : -1.59 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 212 HIS 0.029 0.002 HIS T 70 PHE 0.023 0.003 PHE U 72 TYR 0.023 0.002 TYR J 53 ARG 0.013 0.001 ARG Q 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 396 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.7946 (ppp) cc_final: 0.7684 (ttp) REVERT: D 64 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: D 156 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: D 173 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8005 (mm-40) REVERT: D 181 ASP cc_start: 0.7651 (t0) cc_final: 0.6797 (t0) REVERT: D 200 ASP cc_start: 0.8222 (m-30) cc_final: 0.7808 (m-30) REVERT: E 46 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8743 (mm110) REVERT: E 176 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8169 (p0) REVERT: F 133 GLU cc_start: 0.8267 (mp0) cc_final: 0.7958 (mp0) REVERT: H 6 LEU cc_start: 0.7528 (mt) cc_final: 0.6931 (pp) REVERT: H 41 LYS cc_start: 0.7843 (mttt) cc_final: 0.7285 (tmtt) REVERT: J 49 ASP cc_start: 0.8606 (p0) cc_final: 0.7899 (p0) REVERT: J 67 ASN cc_start: 0.7301 (t0) cc_final: 0.7030 (t0) REVERT: J 102 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8593 (tp30) REVERT: J 114 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9099 (mm) REVERT: K 18 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7224 (tpp80) REVERT: K 86 LEU cc_start: 0.8863 (mm) cc_final: 0.8570 (mm) REVERT: N 24 MET cc_start: 0.8886 (ttm) cc_final: 0.8596 (ttm) REVERT: N 99 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8464 (ptmm) REVERT: O 17 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9362 (mt) REVERT: P 2 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8401 (m-40) REVERT: Q 19 GLN cc_start: 0.8546 (mp10) cc_final: 0.8155 (mp10) REVERT: Q 35 PHE cc_start: 0.9594 (t80) cc_final: 0.9244 (t80) REVERT: Q 93 ILE cc_start: 0.9461 (mm) cc_final: 0.9233 (mt) REVERT: S 46 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9097 (pp) REVERT: S 68 ASP cc_start: 0.9009 (t0) cc_final: 0.8593 (t0) REVERT: S 69 LEU cc_start: 0.8713 (mp) cc_final: 0.8492 (mp) REVERT: S 92 ARG cc_start: 0.8291 (mmp80) cc_final: 0.8081 (mmp80) REVERT: T 56 GLU cc_start: 0.8193 (tp30) cc_final: 0.7533 (mm-30) REVERT: T 70 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.7020 (m170) REVERT: T 77 ARG cc_start: 0.8678 (mtt-85) cc_final: 0.8254 (mmt90) REVERT: V 51 GLN cc_start: 0.7292 (mt0) cc_final: 0.7024 (mt0) REVERT: W 5 ARG cc_start: 0.6617 (ptt90) cc_final: 0.5082 (mpp80) REVERT: X 29 LEU cc_start: 0.9456 (mm) cc_final: 0.9151 (mm) REVERT: Y 1 MET cc_start: 0.8160 (ppp) cc_final: 0.7943 (ppp) REVERT: Y 13 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8172 (mt-10) REVERT: Y 25 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7965 (tp40) REVERT: Y 30 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8911 (mmp) REVERT: Z 28 LEU cc_start: 0.9125 (mp) cc_final: 0.8802 (pt) REVERT: 1 4 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7298 (pp20) REVERT: 3 60 CYS cc_start: 0.9260 (m) cc_final: 0.8949 (m) REVERT: M 91 TYR cc_start: 0.7283 (p90) cc_final: 0.7027 (p90) outliers start: 148 outliers final: 93 residues processed: 489 average time/residue: 0.7764 time to fit residues: 660.3814 Evaluate side-chains 476 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 369 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 446 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 399 optimal weight: 10.0000 chunk 221 optimal weight: 0.3980 chunk 457 optimal weight: 30.0000 chunk 370 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 273 optimal weight: 0.5980 chunk 481 optimal weight: 50.0000 chunk 135 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN E 90 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.575 90338 Z= 0.346 Angle : 0.629 37.263 135960 Z= 0.313 Chirality : 0.034 0.480 17487 Planarity : 0.005 0.073 6684 Dihedral : 23.957 179.306 47159 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.86 % Allowed : 20.06 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.32 (0.15), residues: 2772 helix: 0.24 (0.19), residues: 771 sheet: -0.92 (0.22), residues: 533 loop : -1.46 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 212 HIS 0.005 0.001 HIS T 70 PHE 0.014 0.002 PHE W 17 TYR 0.016 0.001 TYR E 101 ARG 0.010 0.001 ARG Q 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 403 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8429 (pmm) cc_final: 0.8209 (pmm) REVERT: D 11 MET cc_start: 0.7928 (ppp) cc_final: 0.7557 (ttp) REVERT: D 64 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: D 156 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7327 (m-10) REVERT: D 200 ASP cc_start: 0.8263 (m-30) cc_final: 0.7770 (m-30) REVERT: E 150 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8051 (p) REVERT: E 176 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8026 (p0) REVERT: F 133 GLU cc_start: 0.8355 (mp0) cc_final: 0.8052 (mp0) REVERT: H 41 LYS cc_start: 0.7873 (mttt) cc_final: 0.7330 (tmtt) REVERT: J 49 ASP cc_start: 0.8590 (p0) cc_final: 0.7825 (p0) REVERT: J 67 ASN cc_start: 0.7262 (t0) cc_final: 0.6987 (t0) REVERT: J 114 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9229 (mm) REVERT: K 1 MET cc_start: 0.8378 (mmm) cc_final: 0.7821 (mmm) REVERT: K 5 GLN cc_start: 0.7716 (tt0) cc_final: 0.7498 (tt0) REVERT: K 18 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7357 (tpp80) REVERT: K 73 ASP cc_start: 0.8781 (p0) cc_final: 0.7815 (t0) REVERT: K 86 LEU cc_start: 0.8778 (mm) cc_final: 0.8561 (mm) REVERT: N 99 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8590 (ptmm) REVERT: O 17 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9329 (mt) REVERT: P 74 GLN cc_start: 0.8147 (mp10) cc_final: 0.7941 (mp10) REVERT: Q 35 PHE cc_start: 0.9491 (t80) cc_final: 0.9122 (t80) REVERT: Q 58 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8132 (mm-40) REVERT: Q 90 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7487 (p0) REVERT: Q 93 ILE cc_start: 0.9409 (mm) cc_final: 0.9096 (mt) REVERT: S 52 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8537 (mp0) REVERT: S 68 ASP cc_start: 0.8801 (t0) cc_final: 0.8359 (t0) REVERT: S 69 LEU cc_start: 0.8663 (mp) cc_final: 0.8383 (mp) REVERT: T 77 ARG cc_start: 0.8661 (mtt-85) cc_final: 0.8309 (mmt90) REVERT: V 51 GLN cc_start: 0.7211 (mt0) cc_final: 0.6875 (mt0) REVERT: V 56 PHE cc_start: 0.6180 (t80) cc_final: 0.5869 (t80) REVERT: W 5 ARG cc_start: 0.6375 (ptt90) cc_final: 0.5053 (mpp80) REVERT: W 20 GLU cc_start: 0.7663 (tp30) cc_final: 0.7189 (tp30) REVERT: X 29 LEU cc_start: 0.9227 (mm) cc_final: 0.8884 (mm) REVERT: X 45 PHE cc_start: 0.8980 (m-80) cc_final: 0.8750 (m-80) REVERT: X 51 SER cc_start: 0.9262 (t) cc_final: 0.8830 (p) REVERT: X 69 GLU cc_start: 0.9250 (pp20) cc_final: 0.9035 (pp20) REVERT: Y 13 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8100 (mt-10) REVERT: Y 25 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8132 (tp40) REVERT: Y 30 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8903 (mmp) REVERT: 3 44 ARG cc_start: 0.8214 (mmm160) cc_final: 0.8009 (mtp180) REVERT: 3 60 CYS cc_start: 0.9269 (m) cc_final: 0.8922 (m) REVERT: M 91 TYR cc_start: 0.7156 (p90) cc_final: 0.6913 (p90) outliers start: 112 outliers final: 78 residues processed: 473 average time/residue: 0.8103 time to fit residues: 664.6477 Evaluate side-chains 467 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 378 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 102 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 180 optimal weight: 9.9990 chunk 483 optimal weight: 50.0000 chunk 106 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 536 optimal weight: 10.0000 chunk 445 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.573 90338 Z= 0.408 Angle : 0.690 37.337 135960 Z= 0.342 Chirality : 0.036 0.471 17487 Planarity : 0.005 0.071 6684 Dihedral : 23.998 178.660 47159 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 5.78 % Allowed : 19.93 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.43 (0.15), residues: 2772 helix: 0.18 (0.19), residues: 764 sheet: -0.98 (0.22), residues: 516 loop : -1.54 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 212 HIS 0.007 0.001 HIS Q 13 PHE 0.016 0.002 PHE U 72 TYR 0.027 0.002 TYR F 6 ARG 0.011 0.001 ARG Q 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 382 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.7931 (ppp) cc_final: 0.7525 (ttp) REVERT: D 64 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8439 (mt-10) REVERT: D 156 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: D 200 ASP cc_start: 0.8276 (m-30) cc_final: 0.7775 (m-30) REVERT: E 100 MET cc_start: 0.9087 (mmp) cc_final: 0.8863 (mmt) REVERT: E 150 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8221 (p) REVERT: E 176 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8084 (p0) REVERT: F 80 GLN cc_start: 0.9027 (tp40) cc_final: 0.8757 (tp40) REVERT: F 133 GLU cc_start: 0.8361 (mp0) cc_final: 0.7992 (mp0) REVERT: H 29 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: H 41 LYS cc_start: 0.7762 (mttt) cc_final: 0.7241 (tmtt) REVERT: J 49 ASP cc_start: 0.8558 (p0) cc_final: 0.7887 (p0) REVERT: J 67 ASN cc_start: 0.7295 (t0) cc_final: 0.7014 (t0) REVERT: J 92 MET cc_start: 0.8868 (ttm) cc_final: 0.8638 (ttm) REVERT: J 114 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9219 (mm) REVERT: K 1 MET cc_start: 0.8280 (mmm) cc_final: 0.7791 (mmm) REVERT: K 5 GLN cc_start: 0.7580 (tt0) cc_final: 0.7322 (tt0) REVERT: K 18 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7264 (tpp80) REVERT: K 73 ASP cc_start: 0.8854 (p0) cc_final: 0.7945 (t0) REVERT: L 16 LYS cc_start: 0.8393 (mttt) cc_final: 0.7839 (mttt) REVERT: O 17 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9335 (mt) REVERT: Q 35 PHE cc_start: 0.9515 (t80) cc_final: 0.9112 (t80) REVERT: Q 58 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8095 (mm-40) REVERT: Q 90 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7664 (p0) REVERT: S 46 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9070 (pp) REVERT: S 68 ASP cc_start: 0.8800 (t0) cc_final: 0.8346 (t0) REVERT: S 69 LEU cc_start: 0.8648 (mp) cc_final: 0.8410 (mm) REVERT: T 77 ARG cc_start: 0.8627 (mtt-85) cc_final: 0.8277 (mmt90) REVERT: V 51 GLN cc_start: 0.7272 (mt0) cc_final: 0.6946 (mt0) REVERT: W 5 ARG cc_start: 0.6366 (ptt90) cc_final: 0.5229 (mpp80) REVERT: W 20 GLU cc_start: 0.6804 (tp30) cc_final: 0.6298 (tp30) REVERT: X 29 LEU cc_start: 0.9347 (mm) cc_final: 0.8966 (mm) REVERT: X 51 SER cc_start: 0.9294 (t) cc_final: 0.8877 (p) REVERT: X 69 GLU cc_start: 0.9259 (pp20) cc_final: 0.9026 (pp20) REVERT: Y 13 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8166 (mt-10) REVERT: Y 25 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8106 (tp40) REVERT: Y 30 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8926 (mmp) REVERT: 3 60 CYS cc_start: 0.9170 (m) cc_final: 0.8861 (m) REVERT: M 91 TYR cc_start: 0.7188 (p90) cc_final: 0.6961 (p90) outliers start: 133 outliers final: 102 residues processed: 471 average time/residue: 0.7783 time to fit residues: 642.6461 Evaluate side-chains 481 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 367 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 135 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 517 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 chunk 392 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 452 optimal weight: 30.0000 chunk 299 optimal weight: 10.0000 chunk 534 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 overall best weight: 9.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 HIS F 26 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 86 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.573 90338 Z= 0.431 Angle : 0.720 37.421 135960 Z= 0.358 Chirality : 0.038 0.467 17487 Planarity : 0.005 0.071 6684 Dihedral : 24.123 176.012 47159 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 6.38 % Allowed : 20.10 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.15), residues: 2772 helix: 0.01 (0.19), residues: 756 sheet: -1.12 (0.22), residues: 516 loop : -1.62 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 212 HIS 0.009 0.001 HIS Q 13 PHE 0.018 0.002 PHE W 17 TYR 0.018 0.002 TYR J 53 ARG 0.012 0.001 ARG Q 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 393 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: D 156 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7363 (m-10) REVERT: E 100 MET cc_start: 0.9044 (mmp) cc_final: 0.8829 (mmm) REVERT: E 150 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8221 (p) REVERT: E 176 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8147 (p0) REVERT: E 194 LYS cc_start: 0.8231 (mppt) cc_final: 0.7769 (mptt) REVERT: F 80 GLN cc_start: 0.8959 (tp40) cc_final: 0.8704 (tp40) REVERT: F 133 GLU cc_start: 0.8294 (mp0) cc_final: 0.7888 (mp0) REVERT: H 6 LEU cc_start: 0.7803 (mt) cc_final: 0.6976 (pp) REVERT: H 8 LYS cc_start: 0.7523 (mttt) cc_final: 0.6737 (mmmt) REVERT: H 29 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: H 41 LYS cc_start: 0.7832 (mttt) cc_final: 0.7388 (tmtt) REVERT: J 49 ASP cc_start: 0.8508 (p0) cc_final: 0.7775 (p0) REVERT: J 92 MET cc_start: 0.8985 (ttm) cc_final: 0.8628 (ttm) REVERT: J 114 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9208 (mm) REVERT: K 1 MET cc_start: 0.8237 (mmm) cc_final: 0.7539 (mmm) REVERT: K 5 GLN cc_start: 0.7595 (tt0) cc_final: 0.7312 (tt0) REVERT: K 18 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.6787 (tpp80) REVERT: K 20 MET cc_start: 0.7545 (tpt) cc_final: 0.7169 (tpt) REVERT: K 73 ASP cc_start: 0.8906 (p0) cc_final: 0.7973 (t0) REVERT: L 16 LYS cc_start: 0.8427 (mttt) cc_final: 0.7844 (mttt) REVERT: L 46 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6496 (ttm110) REVERT: P 59 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8415 (t) REVERT: Q 19 GLN cc_start: 0.8505 (mp10) cc_final: 0.8147 (mp10) REVERT: Q 35 PHE cc_start: 0.9523 (t80) cc_final: 0.9095 (t80) REVERT: Q 58 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8085 (mm-40) REVERT: Q 90 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7531 (p0) REVERT: S 46 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9026 (pp) REVERT: S 68 ASP cc_start: 0.8916 (t0) cc_final: 0.8431 (t0) REVERT: T 56 GLU cc_start: 0.8064 (tp30) cc_final: 0.7558 (mm-30) REVERT: T 61 LEU cc_start: 0.9090 (pp) cc_final: 0.8886 (pt) REVERT: T 69 ARG cc_start: 0.8703 (ttp-110) cc_final: 0.8317 (ptm-80) REVERT: T 77 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.8229 (mmt90) REVERT: V 51 GLN cc_start: 0.7328 (mt0) cc_final: 0.7033 (mt0) REVERT: W 5 ARG cc_start: 0.6379 (ptt90) cc_final: 0.5338 (mpp80) REVERT: W 12 LEU cc_start: 0.8609 (mm) cc_final: 0.8099 (mm) REVERT: W 20 GLU cc_start: 0.7019 (tp30) cc_final: 0.6529 (tp30) REVERT: X 29 LEU cc_start: 0.9372 (mm) cc_final: 0.9010 (mm) REVERT: Y 13 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8259 (mt-10) REVERT: Y 25 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8020 (tp40) REVERT: Y 30 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8916 (mmp) REVERT: 0 4 GLN cc_start: 0.9212 (tp40) cc_final: 0.8892 (tp40) REVERT: 3 60 CYS cc_start: 0.9146 (m) cc_final: 0.8873 (m) REVERT: M 60 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.6151 (pm20) outliers start: 147 outliers final: 114 residues processed: 491 average time/residue: 0.7699 time to fit residues: 659.2315 Evaluate side-chains 504 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 376 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 56 PHE Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 135 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 330 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 340 optimal weight: 10.0000 chunk 364 optimal weight: 30.0000 chunk 264 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 420 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 86 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.573 90338 Z= 0.416 Angle : 0.707 37.412 135960 Z= 0.351 Chirality : 0.037 0.463 17487 Planarity : 0.005 0.071 6684 Dihedral : 24.130 175.474 47159 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 6.04 % Allowed : 21.93 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.15), residues: 2772 helix: 0.01 (0.19), residues: 756 sheet: -1.16 (0.22), residues: 519 loop : -1.66 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 212 HIS 0.009 0.002 HIS T 70 PHE 0.017 0.002 PHE V 91 TYR 0.018 0.002 TYR K 32 ARG 0.011 0.001 ARG Q 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 386 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: D 156 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: D 200 ASP cc_start: 0.8316 (m-30) cc_final: 0.8105 (m-30) REVERT: E 57 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.6576 (mtmm) REVERT: E 176 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8119 (p0) REVERT: E 194 LYS cc_start: 0.8230 (mppt) cc_final: 0.7761 (mptt) REVERT: F 80 GLN cc_start: 0.8944 (tp40) cc_final: 0.8684 (tp40) REVERT: F 133 GLU cc_start: 0.8301 (mp0) cc_final: 0.7904 (mp0) REVERT: H 6 LEU cc_start: 0.7838 (mt) cc_final: 0.7040 (pp) REVERT: H 29 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: H 41 LYS cc_start: 0.7789 (mttt) cc_final: 0.7328 (tmtt) REVERT: J 9 GLU cc_start: 0.8698 (pm20) cc_final: 0.8446 (pm20) REVERT: J 49 ASP cc_start: 0.8600 (p0) cc_final: 0.7843 (p0) REVERT: J 92 MET cc_start: 0.9054 (ttm) cc_final: 0.8686 (ttm) REVERT: J 114 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9221 (mm) REVERT: K 1 MET cc_start: 0.8048 (mmm) cc_final: 0.7734 (mmm) REVERT: K 5 GLN cc_start: 0.7601 (tt0) cc_final: 0.7309 (tt0) REVERT: K 18 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.6879 (tpp80) REVERT: K 73 ASP cc_start: 0.8896 (p0) cc_final: 0.7960 (t0) REVERT: L 46 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6423 (ttm110) REVERT: P 59 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8421 (t) REVERT: P 99 LEU cc_start: 0.9092 (tt) cc_final: 0.8867 (mp) REVERT: Q 19 GLN cc_start: 0.8618 (mp10) cc_final: 0.8318 (mp10) REVERT: Q 35 PHE cc_start: 0.9514 (t80) cc_final: 0.9090 (t80) REVERT: Q 58 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8130 (mm-40) REVERT: Q 90 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7552 (p0) REVERT: S 68 ASP cc_start: 0.8704 (t0) cc_final: 0.8324 (t0) REVERT: T 24 MET cc_start: 0.7615 (tpp) cc_final: 0.7183 (tpp) REVERT: T 69 ARG cc_start: 0.8701 (ttp-110) cc_final: 0.8322 (ptm-80) REVERT: T 77 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8312 (mmt90) REVERT: W 5 ARG cc_start: 0.6379 (ptt90) cc_final: 0.5318 (mpp80) REVERT: W 20 GLU cc_start: 0.6894 (tp30) cc_final: 0.6356 (tp30) REVERT: X 29 LEU cc_start: 0.9354 (mm) cc_final: 0.8989 (mm) REVERT: Y 13 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8260 (mt-10) REVERT: Y 25 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8102 (tp40) REVERT: Y 30 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8918 (mmp) REVERT: 0 4 GLN cc_start: 0.9202 (tp40) cc_final: 0.8888 (tp40) REVERT: 0 41 HIS cc_start: 0.7211 (m90) cc_final: 0.6916 (m90) REVERT: 3 60 CYS cc_start: 0.9225 (m) cc_final: 0.8948 (m) REVERT: M 60 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.6273 (pm20) outliers start: 139 outliers final: 109 residues processed: 480 average time/residue: 0.7417 time to fit residues: 621.2800 Evaluate side-chains 493 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 371 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 56 PHE Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 31 LEU Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 135 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 486 optimal weight: 20.0000 chunk 512 optimal weight: 50.0000 chunk 467 optimal weight: 10.0000 chunk 498 optimal weight: 20.0000 chunk 300 optimal weight: 20.0000 chunk 217 optimal weight: 40.0000 chunk 391 optimal weight: 10.0000 chunk 152 optimal weight: 0.2980 chunk 450 optimal weight: 20.0000 chunk 471 optimal weight: 20.0000 chunk 496 optimal weight: 40.0000 overall best weight: 12.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 86 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.570 90338 Z= 0.516 Angle : 0.820 37.420 135960 Z= 0.405 Chirality : 0.042 0.452 17487 Planarity : 0.006 0.076 6684 Dihedral : 24.237 176.361 47159 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 31.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.64 % Favored : 89.29 % Rotamer: Outliers : 6.43 % Allowed : 21.88 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.93 (0.15), residues: 2772 helix: -0.27 (0.18), residues: 756 sheet: -1.28 (0.23), residues: 505 loop : -1.84 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 212 HIS 0.009 0.002 HIS T 70 PHE 0.021 0.002 PHE U 72 TYR 0.021 0.003 TYR J 53 ARG 0.012 0.001 ARG Q 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 376 time to evaluate : 5.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8473 (mt-10) REVERT: D 156 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7331 (m-10) REVERT: D 200 ASP cc_start: 0.8303 (m-30) cc_final: 0.8085 (m-30) REVERT: E 57 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.6631 (mtmm) REVERT: E 176 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8200 (p0) REVERT: F 80 GLN cc_start: 0.8977 (tp40) cc_final: 0.8751 (tp40) REVERT: F 133 GLU cc_start: 0.8327 (mp0) cc_final: 0.7879 (mp0) REVERT: H 6 LEU cc_start: 0.7913 (mt) cc_final: 0.6979 (pp) REVERT: H 8 LYS cc_start: 0.7603 (mttt) cc_final: 0.6853 (mmmt) REVERT: H 29 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: H 41 LYS cc_start: 0.7848 (mttt) cc_final: 0.7406 (tmtt) REVERT: J 49 ASP cc_start: 0.8640 (p0) cc_final: 0.7930 (p0) REVERT: J 114 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9197 (mm) REVERT: K 1 MET cc_start: 0.7919 (mmm) cc_final: 0.7714 (mmm) REVERT: K 18 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6863 (tpp80) REVERT: K 20 MET cc_start: 0.7844 (tpt) cc_final: 0.7405 (tpt) REVERT: L 46 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6427 (ttm110) REVERT: P 59 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8450 (t) REVERT: Q 19 GLN cc_start: 0.8623 (mp10) cc_final: 0.8313 (mp10) REVERT: Q 35 PHE cc_start: 0.9496 (t80) cc_final: 0.9061 (t80) REVERT: S 68 ASP cc_start: 0.8874 (t0) cc_final: 0.8492 (t0) REVERT: T 69 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.8328 (ptm-80) REVERT: T 77 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.8237 (mmt90) REVERT: W 5 ARG cc_start: 0.6448 (ptt90) cc_final: 0.5454 (mpp80) REVERT: X 29 LEU cc_start: 0.9383 (mm) cc_final: 0.9012 (mm) REVERT: Y 13 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8309 (mt-10) REVERT: Y 25 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8125 (tp40) REVERT: Y 30 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8945 (mmp) REVERT: 0 4 GLN cc_start: 0.9171 (tp40) cc_final: 0.8835 (tp40) REVERT: 3 60 CYS cc_start: 0.9224 (m) cc_final: 0.8952 (m) REVERT: M 60 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6292 (pm20) REVERT: M 103 TYR cc_start: 0.7567 (m-10) cc_final: 0.7348 (m-10) outliers start: 148 outliers final: 123 residues processed: 477 average time/residue: 0.7691 time to fit residues: 641.8328 Evaluate side-chains 501 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 366 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 56 PHE Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 327 optimal weight: 10.0000 chunk 527 optimal weight: 20.0000 chunk 321 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 552 optimal weight: 20.0000 chunk 508 optimal weight: 20.0000 chunk 440 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 340 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS Q 55 GLN R 18 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.574 90338 Z= 0.398 Angle : 0.698 37.371 135960 Z= 0.346 Chirality : 0.037 0.460 17487 Planarity : 0.005 0.071 6684 Dihedral : 24.203 175.322 47159 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 5.43 % Allowed : 23.58 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.71 (0.15), residues: 2772 helix: -0.03 (0.19), residues: 758 sheet: -1.17 (0.23), residues: 504 loop : -1.72 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 212 HIS 0.020 0.002 HIS T 70 PHE 0.017 0.002 PHE R 53 TYR 0.019 0.002 TYR K 32 ARG 0.011 0.001 ARG Q 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 384 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8432 (mt-10) REVERT: D 156 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: E 57 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.6547 (mtmm) REVERT: E 176 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8092 (p0) REVERT: F 133 GLU cc_start: 0.8268 (mp0) cc_final: 0.7866 (mp0) REVERT: H 6 LEU cc_start: 0.7837 (mt) cc_final: 0.6908 (pp) REVERT: H 8 LYS cc_start: 0.7570 (mttt) cc_final: 0.6841 (mmmt) REVERT: H 29 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: H 41 LYS cc_start: 0.7780 (mttt) cc_final: 0.7416 (tmtt) REVERT: J 49 ASP cc_start: 0.8623 (p0) cc_final: 0.7800 (p0) REVERT: J 114 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9224 (mm) REVERT: K 1 MET cc_start: 0.7861 (mmm) cc_final: 0.7623 (mmm) REVERT: K 18 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6743 (tpp80) REVERT: K 20 MET cc_start: 0.7499 (tpt) cc_final: 0.7177 (tpt) REVERT: K 73 ASP cc_start: 0.8960 (p0) cc_final: 0.7931 (t0) REVERT: L 46 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6412 (ttm110) REVERT: P 99 LEU cc_start: 0.9087 (tt) cc_final: 0.8871 (mp) REVERT: Q 19 GLN cc_start: 0.8589 (mp10) cc_final: 0.8299 (mp10) REVERT: Q 35 PHE cc_start: 0.9514 (t80) cc_final: 0.9096 (t80) REVERT: Q 58 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8169 (mm-40) REVERT: Q 90 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7569 (p0) REVERT: S 68 ASP cc_start: 0.8870 (t0) cc_final: 0.8490 (t0) REVERT: T 24 MET cc_start: 0.7573 (tpp) cc_final: 0.7171 (tpp) REVERT: T 77 ARG cc_start: 0.8599 (mtt-85) cc_final: 0.8350 (mmt90) REVERT: W 5 ARG cc_start: 0.6381 (ptt90) cc_final: 0.5384 (mpp80) REVERT: W 20 GLU cc_start: 0.6261 (tp30) cc_final: 0.5766 (tp30) REVERT: X 29 LEU cc_start: 0.9340 (mm) cc_final: 0.8952 (mm) REVERT: Y 13 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8230 (mt-10) REVERT: Y 25 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8189 (tp40) REVERT: Y 30 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8902 (mmp) REVERT: 0 4 GLN cc_start: 0.9186 (tp40) cc_final: 0.8816 (tp40) REVERT: 3 60 CYS cc_start: 0.9227 (m) cc_final: 0.8944 (m) REVERT: M 60 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.6266 (pm20) outliers start: 125 outliers final: 103 residues processed: 466 average time/residue: 0.7538 time to fit residues: 612.1043 Evaluate side-chains 493 residues out of total 2305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 378 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 77 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 56 PHE Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 73 ILE Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 349 optimal weight: 20.0000 chunk 469 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 405 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 440 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 452 optimal weight: 40.0000 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** 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 = 0.3598 r_free = 0.3598 target = 0.079023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.065265 restraints weight = 499576.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066493 restraints weight = 189961.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067231 restraints weight = 112821.864| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.576 90338 Z= 0.334 Angle : 0.619 37.241 135960 Z= 0.307 Chirality : 0.033 0.487 17487 Planarity : 0.004 0.082 6684 Dihedral : 24.039 176.563 47159 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.56 % Allowed : 24.49 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.43 (0.16), residues: 2772 helix: 0.28 (0.19), residues: 750 sheet: -1.06 (0.22), residues: 524 loop : -1.56 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 212 HIS 0.016 0.001 HIS T 70 PHE 0.014 0.002 PHE R 53 TYR 0.017 0.002 TYR C 102 ARG 0.008 0.001 ARG Q 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12193.00 seconds wall clock time: 221 minutes 34.40 seconds (13294.40 seconds total)