Starting phenix.real_space_refine on Tue Sep 24 10:12:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/09_2024/8bh6_16048.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/09_2024/8bh6_16048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/09_2024/8bh6_16048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/09_2024/8bh6_16048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/09_2024/8bh6_16048.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/09_2024/8bh6_16048.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.108 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 1547 5.49 5 S 49 5.16 5 C 26336 2.51 5 N 9502 2.21 5 O 14114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51548 Number of models: 1 Model: "" Number of chains: 20 Chain: "a" Number of atoms: 33126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1547, 33126 Classifications: {'RNA': 1547} Modifications used: {'rna2p_pur': 123, 'rna2p_pyr': 90, 'rna3p_pur': 744, 'rna3p_pyr': 590} Link IDs: {'rna2p': 213, 'rna3p': 1333} Chain: "b" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1802 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "c" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1634 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain: "d" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1570 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain breaks: 1 Chain: "e" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1234 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "f" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 798 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "g" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1189 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 124} Chain: "i" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 116} Chain: "j" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 95} Chain: "k" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 880 Classifications: {'peptide': 118} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1062 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 126} Chain: "m" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 104} Chain: "n" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 493 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP%COO:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "o" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 738 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 712 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 83} Chain: "q" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 707 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "r" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 585 Classifications: {'peptide': 70} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 64} Chain: "s" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 77} Chain: "t" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'CIS': 1, 'TRANS': 78} Time building chain proxies: 22.03, per 1000 atoms: 0.43 Number of scatterers: 51548 At special positions: 0 Unit cell: (140.4, 199.2, 242.4, 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 49 16.00 P 1547 15.00 O 14114 8.00 N 9502 7.00 C 26336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.51 Conformation dependent library (CDL) restraints added in 2.3 seconds 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4302 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 22 sheets defined 39.5% alpha, 13.9% beta 501 base pairs and 802 stacking pairs defined. Time for finding SS restraints: 18.93 Creating SS restraints... Processing helix chain 'b' and resid 8 through 13 Processing helix chain 'b' and resid 24 through 28 removed outlier: 3.528A pdb=" N MET b 27 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS b 28 " --> pdb=" O PRO b 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 28' Processing helix chain 'b' and resid 43 through 63 removed outlier: 3.815A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP b 63 " --> pdb=" O GLN b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.811A pdb=" N SER b 82 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 120 removed outlier: 3.758A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET b 120 " --> pdb=" O GLU b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 149 removed outlier: 3.672A pdb=" N VAL b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 179 Processing helix chain 'b' and resid 206 through 227 removed outlier: 3.556A pdb=" N GLY b 227 " --> pdb=" O GLU b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 12 Processing helix chain 'c' and resid 28 through 42 Processing helix chain 'c' and resid 42 through 50 removed outlier: 5.072A pdb=" N GLU c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.858A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 95 removed outlier: 3.667A pdb=" N ALA c 92 " --> pdb=" O ASN c 88 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.510A pdb=" N VAL c 115 " --> pdb=" O ASP c 111 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN c 125 " --> pdb=" O ARG c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.574A pdb=" N VAL c 132 " --> pdb=" O SER c 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 62 removed outlier: 4.365A pdb=" N LEU d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 75 removed outlier: 3.869A pdb=" N ASN d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 91 removed outlier: 3.833A pdb=" N ASN d 85 " --> pdb=" O VAL d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 100 Processing helix chain 'd' and resid 106 through 116 removed outlier: 3.965A pdb=" N ALA d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 146 Processing helix chain 'd' and resid 148 through 157 removed outlier: 3.597A pdb=" N GLU d 156 " --> pdb=" O VAL d 152 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 198 removed outlier: 3.700A pdb=" N TYR d 198 " --> pdb=" O ILE d 194 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 68 Processing helix chain 'e' and resid 108 through 118 Processing helix chain 'e' and resid 132 through 146 removed outlier: 3.584A pdb=" N MET e 136 " --> pdb=" O THR e 132 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 155 Processing helix chain 'f' and resid 15 through 32 Processing helix chain 'f' and resid 72 through 79 removed outlier: 3.924A pdb=" N ARG f 78 " --> pdb=" O ASP f 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 31 removed outlier: 3.574A pdb=" N LYS g 25 " --> pdb=" O LYS g 21 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS g 29 " --> pdb=" O LYS g 25 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 53 removed outlier: 3.805A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 69 Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.840A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 128 Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'h' and resid 5 through 19 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 114 through 121 removed outlier: 3.609A pdb=" N ALA h 118 " --> pdb=" O THR h 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 51 removed outlier: 3.907A pdb=" N LEU i 50 " --> pdb=" O LEU i 46 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 57 Processing helix chain 'i' and resid 73 through 79 removed outlier: 3.507A pdb=" N GLN i 77 " --> pdb=" O GLY i 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 93 removed outlier: 3.863A pdb=" N GLY i 84 " --> pdb=" O ALA i 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 95 through 102 removed outlier: 4.335A pdb=" N SER i 99 " --> pdb=" O GLU i 95 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 32 Processing helix chain 'j' and resid 80 through 89 Processing helix chain 'k' and resid 48 through 51 removed outlier: 3.715A pdb=" N GLY k 51 " --> pdb=" O GLY k 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 48 through 51' Processing helix chain 'k' and resid 53 through 58 Processing helix chain 'k' and resid 59 through 78 removed outlier: 3.953A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 90 through 93 removed outlier: 3.686A pdb=" N ARG k 93 " --> pdb=" O GLY k 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 90 through 93' Processing helix chain 'k' and resid 94 through 103 removed outlier: 3.683A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 9 Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.939A pdb=" N GLN m 31 " --> pdb=" O THR m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 60 removed outlier: 3.915A pdb=" N ARG m 55 " --> pdb=" O ASP m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 61 through 63 No H-bonds generated for 'chain 'm' and resid 61 through 63' Processing helix chain 'm' and resid 66 through 83 removed outlier: 4.202A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 91 Processing helix chain 'n' and resid 3 through 10 removed outlier: 4.048A pdb=" N ALA n 8 " --> pdb=" O THR n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 50 Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.740A pdb=" N LYS o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR o 15 " --> pdb=" O ILE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.706A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 74 removed outlier: 3.711A pdb=" N SER o 72 " --> pdb=" O ASN o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.910A pdb=" N ARG o 79 " --> pdb=" O ILE o 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 64 Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'p' and resid 79 through 89 removed outlier: 3.566A pdb=" N LYS p 83 " --> pdb=" O GLY p 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 16 through 21 removed outlier: 3.859A pdb=" N THR r 19 " --> pdb=" O CYS r 16 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA r 20 " --> pdb=" O TYR r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 removed outlier: 3.720A pdb=" N THR r 50 " --> pdb=" O PRO r 46 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 68 removed outlier: 3.932A pdb=" N THR r 62 " --> pdb=" O ARG r 58 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 25 removed outlier: 3.816A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 removed outlier: 3.590A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 41 removed outlier: 3.680A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 62 removed outlier: 4.419A pdb=" N GLU t 48 " --> pdb=" O ASP t 44 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN t 62 " --> pdb=" O ASP t 58 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 79 Processing sheet with id=AA1, first strand: chain 'b' and resid 67 through 69 removed outlier: 5.486A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU b 161 " --> pdb=" O VAL b 184 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE b 186 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL b 163 " --> pdb=" O ILE b 186 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE b 183 " --> pdb=" O TYR b 198 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE b 200 " --> pdb=" O ILE b 183 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY b 185 " --> pdb=" O ILE b 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'c' and resid 54 through 57 removed outlier: 3.557A pdb=" N ILE c 65 " --> pdb=" O HIS c 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 54 through 57 removed outlier: 6.520A pdb=" N ILE c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE c 67 " --> pdb=" O ILE c 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 166 Processing sheet with id=AA5, first strand: chain 'c' and resid 163 through 166 removed outlier: 4.161A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA c 186 " --> pdb=" O VAL c 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 120 through 121 Processing sheet with id=AA7, first strand: chain 'e' and resid 12 through 24 removed outlier: 5.452A pdb=" N GLU e 13 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY e 40 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL e 21 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 85 through 87 removed outlier: 3.584A pdb=" N ILE e 106 " --> pdb=" O ILE e 123 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER e 125 " --> pdb=" O ILE e 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 36 through 37 removed outlier: 4.199A pdb=" N GLU f 36 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS f 66 " --> pdb=" O GLU f 36 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL f 6 " --> pdb=" O VAL f 63 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER f 67 " --> pdb=" O ARG f 2 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET f 90 " --> pdb=" O MET f 7 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE f 9 " --> pdb=" O ARG f 88 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 44 through 47 Processing sheet with id=AB2, first strand: chain 'g' and resid 73 through 78 removed outlier: 3.703A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 24 through 27 removed outlier: 3.559A pdb=" N LEU h 25 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU h 62 " --> pdb=" O LEU h 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.587A pdb=" N TRP h 132 " --> pdb=" O GLY h 76 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 11 through 13 removed outlier: 3.683A pdb=" N VAL i 18 " --> pdb=" O HIS i 70 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS i 70 " --> pdb=" O VAL i 18 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR i 31 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL i 67 " --> pdb=" O THR i 31 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 70 through 76 removed outlier: 3.981A pdb=" N ARG j 9 " --> pdb=" O GLU j 99 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 49 through 52 Processing sheet with id=AB8, first strand: chain 'k' and resid 43 through 46 removed outlier: 3.940A pdb=" N SER k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER k 45 " --> pdb=" O VAL k 32 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL k 32 " --> pdb=" O SER k 45 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY k 19 " --> pdb=" O GLU k 83 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR k 85 " --> pdb=" O GLY k 19 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA k 21 " --> pdb=" O THR k 85 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ARG k 111 " --> pdb=" O VAL k 82 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL k 84 " --> pdb=" O ARG k 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 25 through 26 removed outlier: 3.552A pdb=" N LEU l 38 " --> pdb=" O LYS l 26 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 43 through 53 removed outlier: 7.405A pdb=" N ARG l 67 " --> pdb=" O THR l 48 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL l 50 " --> pdb=" O TYR l 65 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR l 65 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR l 52 " --> pdb=" O ARG l 63 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG l 63 " --> pdb=" O THR l 52 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR l 108 " --> pdb=" O ASN l 77 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR l 79 " --> pdb=" O TYR l 108 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE l 110 " --> pdb=" O TYR l 79 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS l 109 " --> pdb=" O ARG l 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'p' and resid 3 through 9 Processing sheet with id=AC3, first strand: chain 'q' and resid 39 through 43 removed outlier: 4.310A pdb=" N THR q 29 " --> pdb=" O TYR q 42 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE q 75 " --> pdb=" O LYS q 47 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU q 77 " --> pdb=" O HIS q 49 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU q 77 " --> pdb=" O GLN q 64 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN q 64 " --> pdb=" O LEU q 77 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU q 79 " --> pdb=" O LYS q 62 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS q 62 " --> pdb=" O GLU q 79 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE q 60 " --> pdb=" O VAL q 81 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL q 11 " --> pdb=" O GLU q 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU q 28 " --> pdb=" O VAL q 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 's' and resid 48 through 51 removed outlier: 3.889A pdb=" N VAL s 51 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL s 58 " --> pdb=" O VAL s 51 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1237 hydrogen bonds 1974 hydrogen bond angles 0 basepair planarities 501 basepair parallelities 802 stacking parallelities Total time for adding SS restraints: 34.41 Time building geometry restraints manager: 11.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9176 1.33 - 1.46: 22592 1.46 - 1.58: 20819 1.58 - 1.70: 3094 1.70 - 1.83: 90 Bond restraints: 55771 Sorted by residual: bond pdb=" CA ARG i 115 " pdb=" C ARG i 115 " ideal model delta sigma weight residual 1.529 1.453 0.076 1.40e-02 5.10e+03 2.92e+01 bond pdb=" C GLY l 131 " pdb=" N THR l 132 " ideal model delta sigma weight residual 1.330 1.260 0.070 1.32e-02 5.74e+03 2.80e+01 bond pdb=" N ARG i 115 " pdb=" CA ARG i 115 " ideal model delta sigma weight residual 1.456 1.409 0.047 1.20e-02 6.94e+03 1.53e+01 bond pdb=" CA ALA l 23 " pdb=" C ALA l 23 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.47e-02 4.63e+03 1.41e+01 bond pdb=" C ASP e 122 " pdb=" N ILE e 123 " ideal model delta sigma weight residual 1.333 1.301 0.032 9.40e-03 1.13e+04 1.15e+01 ... (remaining 55766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 82809 4.97 - 9.94: 91 9.94 - 14.91: 12 14.91 - 19.88: 2 19.88 - 24.86: 1 Bond angle restraints: 82915 Sorted by residual: angle pdb=" N THR m 43 " pdb=" CA THR m 43 " pdb=" C THR m 43 " ideal model delta sigma weight residual 108.48 83.62 24.86 1.65e+00 3.67e-01 2.27e+02 angle pdb=" N LEU l 24 " pdb=" CA LEU l 24 " pdb=" C LEU l 24 " ideal model delta sigma weight residual 112.54 97.93 14.61 1.22e+00 6.72e-01 1.43e+02 angle pdb=" N ARG n 19 " pdb=" CA ARG n 19 " pdb=" C ARG n 19 " ideal model delta sigma weight residual 112.41 98.52 13.89 1.30e+00 5.92e-01 1.14e+02 angle pdb=" C THR m 43 " pdb=" CA THR m 43 " pdb=" CB THR m 43 " ideal model delta sigma weight residual 114.52 131.93 -17.41 1.81e+00 3.05e-01 9.25e+01 angle pdb=" C ALA t 43 " pdb=" CA ALA t 43 " pdb=" CB ALA t 43 " ideal model delta sigma weight residual 111.60 93.62 17.98 2.00e+00 2.50e-01 8.08e+01 ... (remaining 82910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 31511 35.92 - 71.85: 3703 71.85 - 107.77: 402 107.77 - 143.70: 6 143.70 - 179.62: 13 Dihedral angle restraints: 35635 sinusoidal: 28972 harmonic: 6663 Sorted by residual: dihedral pdb=" C ALA t 43 " pdb=" N ALA t 43 " pdb=" CA ALA t 43 " pdb=" CB ALA t 43 " ideal model delta harmonic sigma weight residual -122.60 -98.55 -24.05 0 2.50e+00 1.60e-01 9.25e+01 dihedral pdb=" O4' U a 572 " pdb=" C1' U a 572 " pdb=" N1 U a 572 " pdb=" C2 U a 572 " ideal model delta sinusoidal sigma weight residual 200.00 22.08 177.92 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C a 491 " pdb=" C1' C a 491 " pdb=" N1 C a 491 " pdb=" C2 C a 491 " ideal model delta sinusoidal sigma weight residual 200.00 29.46 170.54 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 35632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 10257 0.118 - 0.237: 272 0.237 - 0.355: 2 0.355 - 0.473: 1 0.473 - 0.591: 1 Chirality restraints: 10533 Sorted by residual: chirality pdb=" CA ALA t 43 " pdb=" N ALA t 43 " pdb=" C ALA t 43 " pdb=" CB ALA t 43 " both_signs ideal model delta sigma weight residual False 2.48 3.08 -0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CG LEU l 24 " pdb=" CB LEU l 24 " pdb=" CD1 LEU l 24 " pdb=" CD2 LEU l 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" C1' A a1368 " pdb=" O4' A a1368 " pdb=" C2' A a1368 " pdb=" N9 A a1368 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 10530 not shown) Planarity restraints: 4786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE b 200 " 0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO b 201 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO b 201 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO b 201 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY k 90 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO k 91 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO k 91 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO k 91 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN j 78 " -0.061 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO j 79 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO j 79 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO j 79 " -0.049 5.00e-02 4.00e+02 ... (remaining 4783 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 3938 2.70 - 3.25: 52015 3.25 - 3.80: 107717 3.80 - 4.35: 132169 4.35 - 4.90: 176068 Nonbonded interactions: 471907 Sorted by model distance: nonbonded pdb=" O HIS l 90 " pdb=" ND1 HIS l 90 " model vdw 2.148 3.120 nonbonded pdb=" O2' U a1137 " pdb=" O5' U a1138 " model vdw 2.183 3.040 nonbonded pdb=" OP1 C a 122 " pdb=" O2' C a 319 " model vdw 2.200 3.040 nonbonded pdb=" NH1 ARG m 87 " pdb=" O GLY s 68 " model vdw 2.200 3.120 nonbonded pdb=" N2 G a 305 " pdb=" OP2 A a 308 " model vdw 2.203 3.120 ... (remaining 471902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.660 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 112.640 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.140 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 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 0.096 55771 Z= 0.232 Angle : 0.721 24.856 82915 Z= 0.403 Chirality : 0.042 0.591 10533 Planarity : 0.006 0.150 4786 Dihedral : 22.898 179.624 31333 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.35 % Rotamer: Outliers : 1.06 % Allowed : 16.84 % Favored : 82.09 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.16), residues: 2269 helix: -1.02 (0.17), residues: 808 sheet: -2.86 (0.24), residues: 361 loop : -2.75 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 9 HIS 0.020 0.002 HIS o 46 PHE 0.038 0.002 PHE n 44 TYR 0.036 0.002 TYR b 91 ARG 0.013 0.001 ARG i 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 74 MET cc_start: 0.5925 (tpp) cc_final: 0.5699 (tpt) REVERT: g 70 MET cc_start: 0.6176 (ptm) cc_final: 0.5400 (mmt) REVERT: g 116 MET cc_start: 0.2996 (mmp) cc_final: 0.2702 (mmp) REVERT: h 46 ILE cc_start: 0.7190 (mm) cc_final: 0.6947 (mt) REVERT: i 129 PHE cc_start: 0.7270 (m-10) cc_final: 0.6920 (m-80) REVERT: j 66 GLU cc_start: 0.7234 (pm20) cc_final: 0.6852 (pm20) REVERT: k 40 ASN cc_start: 0.6825 (m110) cc_final: 0.6457 (t0) REVERT: l 116 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: l 117 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7120 (m) outliers start: 21 outliers final: 6 residues processed: 226 average time/residue: 0.5173 time to fit residues: 196.1998 Evaluate side-chains 189 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain n residue 57 ARG Chi-restraints excluded: chain s residue 45 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 342 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 15 HIS ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 33 HIS ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 40 ASN l 29 ASN l 39 ASN m 100 GLN o 37 ASN ** o 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 55771 Z= 0.197 Angle : 0.618 10.130 82915 Z= 0.318 Chirality : 0.035 0.288 10533 Planarity : 0.005 0.099 4786 Dihedral : 23.416 178.978 26594 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.09 % Allowed : 15.58 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % 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: -2.64 (0.16), residues: 2269 helix: -0.42 (0.17), residues: 813 sheet: -2.43 (0.24), residues: 377 loop : -2.56 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP f 43 HIS 0.008 0.001 HIS o 46 PHE 0.019 0.002 PHE s 44 TYR 0.018 0.002 TYR m 86 ARG 0.006 0.001 ARG e 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 217 time to evaluate : 2.532 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: symmetry clash revert: symmetry clash REVERT: b 93 ASN cc_start: 0.6032 (OUTLIER) cc_final: 0.5494 (m-40) REVERT: e 29 ARG cc_start: 0.7243 (ttp80) cc_final: 0.7029 (ttp80) REVERT: f 88 ARG cc_start: 0.5949 (mmm160) cc_final: 0.5703 (mmm160) REVERT: g 70 MET cc_start: 0.6209 (ptm) cc_final: 0.5359 (mmt) REVERT: h 10 MET cc_start: 0.7666 (ttt) cc_final: 0.7312 (tmm) REVERT: h 19 MET cc_start: 0.6868 (ppp) cc_final: 0.6103 (ppp) REVERT: h 94 MET cc_start: 0.7337 (ttm) cc_final: 0.6920 (ttm) REVERT: i 15 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7695 (tptp) REVERT: i 129 PHE cc_start: 0.7174 (m-10) cc_final: 0.6779 (m-80) REVERT: j 66 GLU cc_start: 0.6981 (pm20) cc_final: 0.6036 (pm20) REVERT: k 65 MET cc_start: 0.5454 (ppp) cc_final: 0.5234 (ppp) REVERT: k 87 LYS cc_start: 0.7325 (ptmm) cc_final: 0.6527 (pttt) REVERT: o 41 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8756 (mm-30) outliers start: 61 outliers final: 32 residues processed: 257 average time/residue: 0.5348 time to fit residues: 232.4686 Evaluate side-chains 217 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 91 TYR Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain d residue 161 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain i residue 8 TYR Chi-restraints excluded: chain i residue 117 LYS Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 76 ILE Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain s residue 45 ILE Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain s residue 84 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 284 optimal weight: 0.0050 chunk 233 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 6.9990 chunk 370 optimal weight: 5.9990 chunk 305 optimal weight: 30.0000 chunk 340 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 275 optimal weight: 6.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 15 HIS ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 159 GLN b 225 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 40 GLN h 22 HIS i 34 ASN ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 15 ASN ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN s 14 HIS ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 55771 Z= 0.252 Angle : 0.703 8.914 82915 Z= 0.359 Chirality : 0.038 0.336 10533 Planarity : 0.006 0.077 4786 Dihedral : 23.575 178.110 26585 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.11 % Allowed : 16.84 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % 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: -2.56 (0.16), residues: 2269 helix: -0.39 (0.17), residues: 820 sheet: -2.23 (0.25), residues: 370 loop : -2.57 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP f 43 HIS 0.017 0.002 HIS d 82 PHE 0.025 0.003 PHE e 11 TYR 0.020 0.002 TYR g 44 ARG 0.008 0.001 ARG k 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 235 time to evaluate : 2.539 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: b 73 LYS cc_start: 0.6664 (tttt) cc_final: 0.6403 (tttm) REVERT: b 96 TRP cc_start: 0.6922 (t-100) cc_final: 0.6655 (t-100) REVERT: b 154 MET cc_start: 0.7256 (tpt) cc_final: 0.6546 (tpt) REVERT: b 219 ASP cc_start: 0.7832 (m-30) cc_final: 0.7604 (m-30) REVERT: c 141 MET cc_start: 0.7230 (mmm) cc_final: 0.7005 (mmp) REVERT: e 14 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7741 (tpp80) REVERT: e 25 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7695 (p) REVERT: e 96 MET cc_start: 0.7083 (mtp) cc_final: 0.6852 (mtm) REVERT: e 145 GLN cc_start: 0.8594 (mm110) cc_final: 0.8348 (mm110) REVERT: g 70 MET cc_start: 0.6080 (ptm) cc_final: 0.5402 (mmt) REVERT: g 116 MET cc_start: 0.2065 (mmp) cc_final: 0.1678 (mmp) REVERT: h 10 MET cc_start: 0.8063 (ttt) cc_final: 0.7744 (tmm) REVERT: h 19 MET cc_start: 0.7197 (ppp) cc_final: 0.6954 (ppp) REVERT: h 86 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7724 (ttm110) REVERT: i 15 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7759 (mttp) REVERT: j 1 MET cc_start: 0.5140 (tmm) cc_final: 0.4728 (tmm) REVERT: j 32 SER cc_start: 0.1887 (p) cc_final: 0.1288 (m) REVERT: j 58 TYR cc_start: 0.5220 (m-80) cc_final: 0.4435 (m-10) REVERT: j 64 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7248 (mm110) REVERT: k 24 ARG cc_start: 0.6529 (mtm-85) cc_final: 0.5702 (mtp180) REVERT: k 87 LYS cc_start: 0.7176 (ptmm) cc_final: 0.6613 (mtmt) REVERT: l 25 ASN cc_start: 0.6866 (OUTLIER) cc_final: 0.6554 (p0) REVERT: n 13 LYS cc_start: 0.6735 (mmmt) cc_final: 0.6371 (mttt) REVERT: o 28 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7807 (tp-100) REVERT: o 37 ASN cc_start: 0.8241 (m110) cc_final: 0.7327 (t0) REVERT: o 41 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8288 (mm-30) REVERT: q 19 MET cc_start: 0.8055 (pmm) cc_final: 0.7843 (pmm) REVERT: t 59 LYS cc_start: 0.6171 (mttt) cc_final: 0.5747 (mmtt) outliers start: 101 outliers final: 58 residues processed: 307 average time/residue: 0.5671 time to fit residues: 292.0042 Evaluate side-chains 256 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 193 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 91 TYR Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 165 ASP Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 161 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 31 ASN Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 86 ARG Chi-restraints excluded: chain i residue 8 TYR Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 76 ILE Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 43 ASN Chi-restraints excluded: chain s residue 61 TYR Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 49 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 344 optimal weight: 0.6980 chunk 364 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 225 GLN d 70 ASN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 ASN f 69 ASN h 31 ASN h 57 GLN l 90 HIS ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 ASN q 53 ASN s 14 HIS ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 55771 Z= 0.298 Angle : 0.762 13.733 82915 Z= 0.385 Chirality : 0.040 0.379 10533 Planarity : 0.007 0.142 4786 Dihedral : 23.860 179.900 26583 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 4.70 % Allowed : 19.63 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.75 (0.16), residues: 2269 helix: -0.64 (0.17), residues: 823 sheet: -2.38 (0.25), residues: 364 loop : -2.57 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP d 9 HIS 0.034 0.003 HIS o 42 PHE 0.027 0.003 PHE d 86 TYR 0.037 0.003 TYR q 30 ARG 0.014 0.001 ARG b 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 215 time to evaluate : 2.519 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: e 41 ASP cc_start: 0.8358 (p0) cc_final: 0.8135 (p0) REVERT: f 90 MET cc_start: 0.3761 (mmt) cc_final: 0.2154 (mpp) REVERT: g 70 MET cc_start: 0.5861 (ptm) cc_final: 0.5393 (mmt) REVERT: g 116 MET cc_start: 0.2198 (mmp) cc_final: 0.1902 (mmp) REVERT: h 10 MET cc_start: 0.8030 (ttt) cc_final: 0.7775 (tmm) REVERT: j 1 MET cc_start: 0.4740 (tmm) cc_final: 0.4436 (tmm) REVERT: l 136 LYS cc_start: 0.5983 (mttp) cc_final: 0.5777 (mptt) REVERT: o 17 VAL cc_start: 0.7527 (m) cc_final: 0.7271 (t) REVERT: p 39 THR cc_start: 0.8360 (t) cc_final: 0.8118 (m) REVERT: s 14 HIS cc_start: 0.1665 (OUTLIER) cc_final: 0.1386 (t70) REVERT: s 26 GLU cc_start: 0.7932 (tt0) cc_final: 0.7411 (tm-30) REVERT: s 27 LYS cc_start: 0.4029 (mttt) cc_final: 0.1343 (pttp) REVERT: s 74 PHE cc_start: 0.5295 (OUTLIER) cc_final: 0.4885 (p90) REVERT: t 72 ASP cc_start: 0.7695 (t0) cc_final: 0.7490 (t70) outliers start: 93 outliers final: 53 residues processed: 288 average time/residue: 0.5386 time to fit residues: 258.1867 Evaluate side-chains 233 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 178 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 91 TYR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain b residue 225 GLN Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 23 TYR Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 4 TYR Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 31 ASN Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 72 HIS Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 74 PHE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 49 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 0.1980 chunk 327 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 75 GLN ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 225 GLN c 175 HIS d 40 GLN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 61 ASN g 68 ASN h 31 ASN h 57 GLN i 83 HIS l 90 HIS ** o 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN s 14 HIS ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 55771 Z= 0.259 Angle : 0.695 10.806 82915 Z= 0.354 Chirality : 0.038 0.288 10533 Planarity : 0.006 0.055 4786 Dihedral : 23.712 178.720 26583 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.15 % Favored : 91.80 % Rotamer: Outliers : 5.36 % Allowed : 20.38 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % 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: -2.57 (0.17), residues: 2269 helix: -0.46 (0.17), residues: 821 sheet: -2.30 (0.25), residues: 373 loop : -2.48 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 200 HIS 0.031 0.002 HIS s 14 PHE 0.044 0.003 PHE b 56 TYR 0.027 0.002 TYR q 30 ARG 0.007 0.001 ARG k 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 186 time to evaluate : 2.456 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: b 90 PHE cc_start: 0.2809 (OUTLIER) cc_final: 0.2570 (p90) REVERT: b 152 ARG cc_start: 0.7447 (mtp180) cc_final: 0.7028 (ttt180) REVERT: e 145 GLN cc_start: 0.8464 (mm110) cc_final: 0.8183 (mm110) REVERT: f 90 MET cc_start: 0.3194 (mmt) cc_final: 0.2895 (mmt) REVERT: g 57 ASP cc_start: 0.7004 (m-30) cc_final: 0.6777 (t70) REVERT: g 70 MET cc_start: 0.5753 (ptm) cc_final: 0.5355 (mmt) REVERT: h 10 MET cc_start: 0.8025 (ttt) cc_final: 0.7734 (tmm) REVERT: i 116 LYS cc_start: 0.7282 (tttm) cc_final: 0.7074 (tmtt) REVERT: j 1 MET cc_start: 0.4706 (tmm) cc_final: 0.4194 (tmm) REVERT: j 73 LEU cc_start: 0.9017 (tp) cc_final: 0.8703 (pp) REVERT: l 136 LYS cc_start: 0.5433 (mttp) cc_final: 0.5124 (mptt) REVERT: m 76 ASN cc_start: 0.6888 (m110) cc_final: 0.6653 (m110) REVERT: o 28 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: o 31 VAL cc_start: 0.5944 (OUTLIER) cc_final: 0.5482 (m) REVERT: p 39 THR cc_start: 0.8374 (t) cc_final: 0.8152 (m) REVERT: p 74 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6459 (pp) REVERT: r 43 LYS cc_start: 0.1356 (OUTLIER) cc_final: 0.1099 (tppt) REVERT: s 16 MET cc_start: 0.5276 (mmm) cc_final: 0.5068 (mmm) REVERT: s 27 LYS cc_start: 0.3697 (mttt) cc_final: 0.1382 (pttp) REVERT: s 74 PHE cc_start: 0.5018 (OUTLIER) cc_final: 0.4608 (p90) REVERT: t 22 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8631 (tp) outliers start: 106 outliers final: 63 residues processed: 271 average time/residue: 0.5283 time to fit residues: 238.8816 Evaluate side-chains 238 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 168 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 91 TYR Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 157 MET Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 149 ASN Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 4 TYR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 63 PHE Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 31 VAL Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 72 HIS Chi-restraints excluded: chain p residue 74 ILE Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 43 LYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 74 PHE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 49 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 20.0000 chunk 328 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 364 optimal weight: 0.9980 chunk 302 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 191 optimal weight: 0.1980 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 75 GLN ** c 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN g 67 ASN g 106 ASN g 129 ASN k 22 HIS l 25 ASN l 90 HIS ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.7447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 55771 Z= 0.220 Angle : 0.648 11.767 82915 Z= 0.330 Chirality : 0.036 0.282 10533 Planarity : 0.005 0.087 4786 Dihedral : 23.587 179.278 26583 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.86 % Allowed : 21.09 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % 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: -2.45 (0.17), residues: 2269 helix: -0.25 (0.18), residues: 818 sheet: -2.28 (0.26), residues: 363 loop : -2.50 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 9 HIS 0.014 0.002 HIS l 90 PHE 0.035 0.002 PHE b 56 TYR 0.021 0.002 TYR q 30 ARG 0.005 0.001 ARG r 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 192 time to evaluate : 2.490 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: symmetry clash revert: symmetry clash REVERT: b 89 GLN cc_start: 0.4867 (mm-40) cc_final: 0.4592 (mp10) REVERT: b 113 ARG cc_start: 0.5318 (mtm180) cc_final: 0.5040 (mtm180) REVERT: g 57 ASP cc_start: 0.7056 (m-30) cc_final: 0.6850 (t70) REVERT: g 70 MET cc_start: 0.5513 (ptm) cc_final: 0.5196 (mmt) REVERT: g 116 MET cc_start: 0.2400 (mmp) cc_final: 0.2057 (mmp) REVERT: h 94 MET cc_start: 0.7881 (ttm) cc_final: 0.7468 (ttm) REVERT: j 73 LEU cc_start: 0.8925 (tp) cc_final: 0.8521 (pp) REVERT: k 44 TRP cc_start: 0.4254 (OUTLIER) cc_final: 0.4051 (p-90) REVERT: k 75 MET cc_start: 0.5847 (mmt) cc_final: 0.5550 (mmp) REVERT: l 136 LYS cc_start: 0.5335 (mttp) cc_final: 0.4793 (mptt) REVERT: o 28 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7104 (mp10) REVERT: p 39 THR cc_start: 0.8401 (t) cc_final: 0.8177 (m) REVERT: q 76 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5916 (tpt-90) REVERT: r 72 LEU cc_start: 0.3849 (mt) cc_final: 0.3491 (mt) REVERT: s 26 GLU cc_start: 0.7855 (tt0) cc_final: 0.6804 (tm-30) REVERT: s 27 LYS cc_start: 0.3647 (mttt) cc_final: 0.1278 (pttp) REVERT: s 74 PHE cc_start: 0.5081 (OUTLIER) cc_final: 0.4770 (p90) REVERT: t 28 MET cc_start: 0.8519 (mmm) cc_final: 0.8155 (mmm) outliers start: 96 outliers final: 64 residues processed: 270 average time/residue: 0.6126 time to fit residues: 280.3046 Evaluate side-chains 239 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 171 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 91 TYR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 157 MET Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain d residue 5 ARG Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 71 LEU Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 136 MET Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 4 TYR Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 77 GLN Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 22 HIS Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 44 TRP Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 72 HIS Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 49 HIS Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 74 PHE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 49 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 307 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 363 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 89 GLN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN j 56 HIS ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 5 ASN q 53 ASN ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.7843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 55771 Z= 0.209 Angle : 0.640 10.754 82915 Z= 0.326 Chirality : 0.035 0.289 10533 Planarity : 0.005 0.056 4786 Dihedral : 23.519 179.749 26583 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.64 % Favored : 91.32 % Rotamer: Outliers : 4.15 % Allowed : 21.90 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % 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: -2.42 (0.17), residues: 2269 helix: -0.21 (0.17), residues: 826 sheet: -2.27 (0.26), residues: 364 loop : -2.50 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP d 9 HIS 0.032 0.002 HIS l 90 PHE 0.037 0.002 PHE b 56 TYR 0.021 0.002 TYR q 30 ARG 0.009 0.001 ARG f 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 189 time to evaluate : 2.512 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: b 152 ARG cc_start: 0.7237 (mtp180) cc_final: 0.6611 (mpt90) REVERT: e 41 ASP cc_start: 0.8554 (p0) cc_final: 0.8196 (p0) REVERT: e 145 GLN cc_start: 0.8419 (mm110) cc_final: 0.8126 (mm110) REVERT: f 27 ASN cc_start: 0.7476 (m110) cc_final: 0.7275 (p0) REVERT: g 70 MET cc_start: 0.5450 (ptm) cc_final: 0.5089 (mmt) REVERT: g 116 MET cc_start: 0.2339 (mmp) cc_final: 0.2029 (mmp) REVERT: j 68 ARG cc_start: 0.4915 (ttp80) cc_final: 0.4566 (ttp80) REVERT: j 73 LEU cc_start: 0.8970 (tp) cc_final: 0.8526 (pp) REVERT: k 75 MET cc_start: 0.6068 (mmt) cc_final: 0.5833 (mmp) REVERT: k 84 VAL cc_start: 0.7579 (t) cc_final: 0.7341 (m) REVERT: l 136 LYS cc_start: 0.5078 (mttp) cc_final: 0.4469 (mptt) REVERT: o 28 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: o 31 VAL cc_start: 0.5801 (OUTLIER) cc_final: 0.5263 (m) REVERT: p 39 THR cc_start: 0.8436 (t) cc_final: 0.8209 (m) REVERT: r 70 MET cc_start: 0.0961 (tpp) cc_final: 0.0554 (tpp) REVERT: s 16 MET cc_start: 0.4481 (mmm) cc_final: 0.4218 (mmm) REVERT: s 26 GLU cc_start: 0.7805 (tt0) cc_final: 0.6780 (tm-30) REVERT: s 27 LYS cc_start: 0.3704 (mttt) cc_final: 0.1358 (pttp) REVERT: s 74 PHE cc_start: 0.4961 (OUTLIER) cc_final: 0.4669 (p90) REVERT: t 28 MET cc_start: 0.8380 (mmm) cc_final: 0.7991 (mmm) outliers start: 82 outliers final: 66 residues processed: 257 average time/residue: 0.5312 time to fit residues: 228.3175 Evaluate side-chains 245 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 176 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 91 TYR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain d residue 5 ARG Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 71 LEU Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 4 TYR Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 77 GLN Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 31 VAL Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 72 HIS Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 49 HIS Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 74 PHE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 89 GLN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 ASN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN k 22 HIS l 90 HIS m 31 GLN ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.9079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 55771 Z= 0.390 Angle : 0.887 12.654 82915 Z= 0.446 Chirality : 0.045 0.385 10533 Planarity : 0.007 0.060 4786 Dihedral : 24.077 179.115 26583 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 32.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.33 % Favored : 88.63 % Rotamer: Outliers : 5.06 % Allowed : 22.21 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % 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: -2.97 (0.16), residues: 2269 helix: -0.81 (0.17), residues: 840 sheet: -2.39 (0.26), residues: 372 loop : -2.78 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP s 34 HIS 0.015 0.002 HIS l 90 PHE 0.035 0.003 PHE b 56 TYR 0.033 0.003 TYR q 30 ARG 0.031 0.001 ARG f 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 178 time to evaluate : 2.575 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: b 22 ARG cc_start: 0.5936 (ttp-170) cc_final: 0.5618 (tpp-160) REVERT: b 152 ARG cc_start: 0.7106 (mtp180) cc_final: 0.6723 (mpt90) REVERT: c 172 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8001 (m) REVERT: d 59 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.5386 (m-80) REVERT: e 145 GLN cc_start: 0.8221 (mm110) cc_final: 0.7925 (mm110) REVERT: g 70 MET cc_start: 0.5559 (ptm) cc_final: 0.5070 (mmt) REVERT: g 116 MET cc_start: 0.2841 (mmp) cc_final: 0.2543 (mmp) REVERT: g 136 LYS cc_start: 0.8283 (mttp) cc_final: 0.7904 (ttpp) REVERT: j 1 MET cc_start: 0.5523 (tmm) cc_final: 0.5301 (tmm) REVERT: k 23 ILE cc_start: 0.9277 (mm) cc_final: 0.8962 (mp) REVERT: n 56 VAL cc_start: 0.6791 (OUTLIER) cc_final: 0.6584 (m) REVERT: p 39 THR cc_start: 0.8644 (t) cc_final: 0.8374 (m) REVERT: r 72 LEU cc_start: 0.4251 (mt) cc_final: 0.3916 (mt) REVERT: s 16 MET cc_start: 0.4072 (mmm) cc_final: 0.3791 (mmm) REVERT: s 27 LYS cc_start: 0.4297 (mttt) cc_final: 0.1963 (pttm) REVERT: t 28 MET cc_start: 0.8666 (mmm) cc_final: 0.8383 (mmm) REVERT: t 72 ASP cc_start: 0.8000 (m-30) cc_final: 0.7349 (t0) outliers start: 100 outliers final: 74 residues processed: 261 average time/residue: 0.5369 time to fit residues: 234.9912 Evaluate side-chains 243 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 166 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 5 ARG Chi-restraints excluded: chain d residue 59 TYR Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 4 TYR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 44 TRP Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 49 HIS Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 74 PHE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 3.9990 chunk 348 optimal weight: 4.9990 chunk 317 optimal weight: 8.9990 chunk 338 optimal weight: 0.1980 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 305 optimal weight: 7.9990 chunk 320 optimal weight: 2.9990 chunk 337 optimal weight: 2.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 16 ASN l 90 HIS ** o 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.9141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 55771 Z= 0.207 Angle : 0.666 11.990 82915 Z= 0.340 Chirality : 0.036 0.293 10533 Planarity : 0.005 0.057 4786 Dihedral : 23.737 179.635 26583 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.55 % Favored : 91.41 % Rotamer: Outliers : 3.64 % Allowed : 23.77 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.61 (0.17), residues: 2269 helix: -0.40 (0.17), residues: 829 sheet: -2.38 (0.26), residues: 369 loop : -2.59 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP s 34 HIS 0.018 0.002 HIS l 90 PHE 0.035 0.002 PHE b 56 TYR 0.022 0.002 TYR q 30 ARG 0.005 0.001 ARG d 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 187 time to evaluate : 2.500 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: b 152 ARG cc_start: 0.7436 (mtp180) cc_final: 0.6838 (mpt90) REVERT: b 154 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6483 (tpt) REVERT: c 160 ASP cc_start: 0.7760 (t0) cc_final: 0.7319 (m-30) REVERT: d 59 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5179 (m-80) REVERT: e 145 GLN cc_start: 0.8336 (mm110) cc_final: 0.8060 (mm110) REVERT: g 70 MET cc_start: 0.5808 (ptm) cc_final: 0.5395 (mmt) REVERT: g 116 MET cc_start: 0.2483 (mmp) cc_final: 0.2151 (mmp) REVERT: g 136 LYS cc_start: 0.8326 (mttp) cc_final: 0.7982 (ttpp) REVERT: j 1 MET cc_start: 0.4652 (tmm) cc_final: 0.4160 (tmm) REVERT: j 58 TYR cc_start: 0.5219 (OUTLIER) cc_final: 0.4149 (m-80) REVERT: k 68 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8403 (pp20) REVERT: r 70 MET cc_start: 0.2320 (tpp) cc_final: 0.1640 (tpp) REVERT: r 72 LEU cc_start: 0.4878 (mt) cc_final: 0.4296 (mt) REVERT: s 16 MET cc_start: 0.4377 (mmm) cc_final: 0.4156 (mmm) REVERT: s 27 LYS cc_start: 0.4323 (mttt) cc_final: 0.2125 (pttm) REVERT: t 28 MET cc_start: 0.8597 (mmm) cc_final: 0.8306 (mmm) REVERT: t 72 ASP cc_start: 0.7827 (m-30) cc_final: 0.7224 (t0) outliers start: 72 outliers final: 64 residues processed: 245 average time/residue: 0.5356 time to fit residues: 221.2153 Evaluate side-chains 242 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 175 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain d residue 5 ARG Chi-restraints excluded: chain d residue 59 TYR Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 82 HIS Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 4 TYR Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 67 SER Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 44 TRP Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 49 HIS Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 74 PHE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 16 LYS Chi-restraints excluded: chain t residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 7.9990 chunk 358 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 248 optimal weight: 0.9980 chunk 375 optimal weight: 0.3980 chunk 345 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 GLN j 56 HIS l 90 HIS ** o 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.9290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 55771 Z= 0.161 Angle : 0.607 11.317 82915 Z= 0.310 Chirality : 0.034 0.428 10533 Planarity : 0.005 0.074 4786 Dihedral : 23.438 179.412 26583 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.07 % Favored : 91.89 % Rotamer: Outliers : 2.83 % Allowed : 24.73 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % Twisted Proline : 1.22 % 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: -2.40 (0.17), residues: 2269 helix: -0.24 (0.17), residues: 836 sheet: -2.21 (0.25), residues: 376 loop : -2.48 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP s 34 HIS 0.024 0.001 HIS l 90 PHE 0.044 0.002 PHE k 61 TYR 0.025 0.002 TYR b 91 ARG 0.020 0.001 ARG f 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4538 Ramachandran restraints generated. 2269 Oldfield, 0 Emsley, 2269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 200 time to evaluate : 2.483 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: b 6 MET cc_start: 0.6069 (tmm) cc_final: 0.5742 (tmm) REVERT: b 90 PHE cc_start: 0.3616 (p90) cc_final: 0.2587 (p90) REVERT: b 152 ARG cc_start: 0.7567 (mtp180) cc_final: 0.6933 (mpt90) REVERT: b 154 MET cc_start: 0.7054 (tpt) cc_final: 0.6056 (tpt) REVERT: c 160 ASP cc_start: 0.7697 (t0) cc_final: 0.7324 (m-30) REVERT: e 41 ASP cc_start: 0.8272 (p0) cc_final: 0.7756 (p0) REVERT: g 70 MET cc_start: 0.5990 (ptm) cc_final: 0.5557 (mmt) REVERT: g 116 MET cc_start: 0.2023 (mmp) cc_final: 0.1653 (mmp) REVERT: g 136 LYS cc_start: 0.8358 (mttp) cc_final: 0.8115 (pttm) REVERT: i 47 ILE cc_start: 0.7710 (mp) cc_final: 0.7476 (mm) REVERT: j 1 MET cc_start: 0.4834 (tmm) cc_final: 0.4330 (tmm) REVERT: j 27 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: k 68 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8402 (pp20) REVERT: o 7 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8176 (ttp80) REVERT: q 19 MET cc_start: 0.8024 (pmm) cc_final: 0.7195 (pmm) REVERT: q 28 GLU cc_start: 0.8156 (tp30) cc_final: 0.7921 (mm-30) REVERT: q 57 LEU cc_start: 0.9012 (tp) cc_final: 0.8784 (mp) REVERT: r 70 MET cc_start: 0.3288 (tpp) cc_final: 0.2556 (tpp) REVERT: r 72 LEU cc_start: 0.4840 (mt) cc_final: 0.4342 (mt) REVERT: s 16 MET cc_start: 0.4433 (mmm) cc_final: 0.4192 (mmm) REVERT: s 26 GLU cc_start: 0.7755 (tt0) cc_final: 0.7300 (tm-30) REVERT: s 27 LYS cc_start: 0.4114 (mttt) cc_final: 0.1890 (pttm) REVERT: t 28 MET cc_start: 0.8497 (mmm) cc_final: 0.8171 (mmm) REVERT: t 72 ASP cc_start: 0.7719 (m-30) cc_final: 0.7499 (m-30) outliers start: 56 outliers final: 49 residues processed: 245 average time/residue: 0.5302 time to fit residues: 217.6017 Evaluate side-chains 231 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 181 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain d residue 5 ARG Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 4 TYR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 44 TRP Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 37 ASN Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 49 GLU Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 74 PHE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 0.6980 chunk 318 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 299 optimal weight: 0.0370 chunk 125 optimal weight: 10.0000 chunk 307 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 4.3466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 89 GLN ** c 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 GLN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 GLN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS t 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.067239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.055293 restraints weight = 449953.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.056640 restraints weight = 221342.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.057380 restraints weight = 150693.074| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.9732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 55771 Z= 0.279 Angle : 0.730 13.515 82915 Z= 0.369 Chirality : 0.038 0.306 10533 Planarity : 0.006 0.057 4786 Dihedral : 23.702 179.742 26583 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.87 % Favored : 90.08 % Rotamer: Outliers : 3.24 % Allowed : 24.58 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.61 (0.17), residues: 2269 helix: -0.48 (0.17), residues: 846 sheet: -2.23 (0.26), residues: 371 loop : -2.59 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP s 34 HIS 0.027 0.002 HIS l 90 PHE 0.034 0.003 PHE b 56 TYR 0.026 0.002 TYR q 30 ARG 0.020 0.001 ARG f 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6743.89 seconds wall clock time: 121 minutes 24.43 seconds (7284.43 seconds total)