Starting phenix.real_space_refine on Mon Mar 25 21:16:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/03_2024/8bh6_16048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/03_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_16048/03_2024/8bh6_16048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/03_2024/8bh6_16048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/03_2024/8bh6_16048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh6_16048/03_2024/8bh6_16048.pdb" } 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 Residue "b GLU 11": "OE1" <-> "OE2" Residue "b GLU 34": "OE1" <-> "OE2" Residue "b GLU 116": "OE1" <-> "OE2" Residue "b GLU 169": "OE1" <-> "OE2" Residue "b GLU 175": "OE1" <-> "OE2" Residue "c GLU 25": "OE1" <-> "OE2" Residue "c GLU 124": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "d GLU 27": "OE1" <-> "OE2" Residue "d GLU 156": "OE1" <-> "OE2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e GLU 13": "OE1" <-> "OE2" Residue "e GLU 58": "OE1" <-> "OE2" Residue "e GLU 78": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "h GLU 23": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 110": "OE1" <-> "OE2" Residue "i GLU 7": "OE1" <-> "OE2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 89": "OE1" <-> "OE2" Residue "l ASP 116": "OD1" <-> "OD2" Residue "m GLU 72": "OE1" <-> "OE2" Residue "n GLU 20": "OE1" <-> "OE2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "q GLU 28": "OE1" <-> "OE2" Residue "q GLU 65": "OE1" <-> "OE2" Residue "q GLU 79": "OE1" <-> "OE2" Residue "s GLU 13": "OE1" <-> "OE2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "t GLU 48": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 27.88, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.43 Conformation dependent library (CDL) restraints added in 4.0 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: 21.51 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: 46.03 Time building geometry restraints manager: 30.05 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: 83.62 - 93.83: 2 93.83 - 104.03: 5511 104.03 - 114.23: 38925 114.23 - 124.44: 31848 124.44 - 134.64: 6629 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 2.520 nonbonded pdb=" O2' U a1137 " pdb=" O5' U a1138 " model vdw 2.183 2.440 nonbonded pdb=" OP1 C a 122 " pdb=" O2' C a 319 " model vdw 2.200 2.440 nonbonded pdb=" NH1 ARG m 87 " pdb=" O GLY s 68 " model vdw 2.200 2.520 nonbonded pdb=" N2 G a 305 " pdb=" OP2 A a 308 " model vdw 2.203 2.520 ... (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 ========== 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: 4.010 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: 0.040 Extract box with map and model: 15.210 Check model and map are aligned: 0.870 Set scattering table: 0.540 Process input model: 173.230 Find NCS groups from input model: 1.090 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.130 ------------------------------------------------------------------------------- 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 : 3.202 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: 0.6434 time to fit residues: 243.2996 Evaluate side-chains 189 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 3.514 ------------------------------------------------------------------------------- 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: 8.9990 chunk 285 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 159 GLN b 225 GLN d 112 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 GLN ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 40 GLN h 22 HIS h 31 ASN i 83 HIS k 40 ASN l 29 ASN ** l 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 100 GLN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** 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 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 14 HIS s 43 ASN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 55771 Z= 0.342 Angle : 0.861 12.529 82915 Z= 0.433 Chirality : 0.045 0.483 10533 Planarity : 0.007 0.097 4786 Dihedral : 23.877 178.822 26594 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 32.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.95 % Favored : 91.01 % Rotamer: Outliers : 5.82 % Allowed : 16.84 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.86 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.13 (0.16), residues: 2269 helix: -0.93 (0.17), residues: 823 sheet: -2.70 (0.23), residues: 371 loop : -2.78 (0.17), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP f 43 HIS 0.010 0.002 HIS s 69 PHE 0.035 0.003 PHE s 44 TYR 0.032 0.003 TYR g 44 ARG 0.011 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 335 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 220 time to evaluate : 3.287 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 73 LYS cc_start: 0.6298 (tttt) cc_final: 0.6095 (tttm) REVERT: b 101 LEU cc_start: 0.8303 (tp) cc_final: 0.8095 (tp) REVERT: b 154 MET cc_start: 0.6905 (tpt) cc_final: 0.6334 (tpt) REVERT: b 219 ASP cc_start: 0.7598 (m-30) cc_final: 0.7331 (m-30) REVERT: c 141 MET cc_start: 0.8044 (mmm) cc_final: 0.7834 (mmm) REVERT: e 25 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.7425 (p) REVERT: e 145 GLN cc_start: 0.8420 (mm110) cc_final: 0.8187 (mm110) REVERT: f 7 MET cc_start: 0.1497 (tmm) cc_final: 0.1193 (tmm) REVERT: g 70 MET cc_start: 0.6250 (ptm) cc_final: 0.5602 (mmt) REVERT: h 46 ILE cc_start: 0.7303 (mm) cc_final: 0.7078 (mm) REVERT: h 86 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7911 (ttm110) REVERT: h 94 MET cc_start: 0.7649 (ttm) cc_final: 0.7176 (ttm) REVERT: i 116 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6581 (tmtt) REVERT: i 129 PHE cc_start: 0.7169 (m-10) cc_final: 0.6768 (m-80) REVERT: j 64 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: j 73 LEU cc_start: 0.8999 (tp) cc_final: 0.8313 (pp) REVERT: k 24 ARG cc_start: 0.6950 (mtm-85) cc_final: 0.5726 (mtt180) REVERT: k 87 LYS cc_start: 0.7646 (ptmm) cc_final: 0.7091 (pttt) REVERT: o 17 VAL cc_start: 0.7733 (m) cc_final: 0.7294 (t) REVERT: o 41 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8784 (mm-30) REVERT: s 26 GLU cc_start: 0.7911 (tt0) cc_final: 0.7625 (tm-30) outliers start: 115 outliers final: 63 residues processed: 310 average time/residue: 0.6415 time to fit residues: 333.1164 Evaluate side-chains 247 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 180 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 41 ILE 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 163 VAL Chi-restraints excluded: chain b residue 165 ASP Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 157 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain f residue 3 THR 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 4 THR Chi-restraints excluded: chain h residue 31 ASN Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 86 ARG Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 8 TYR Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 116 LYS 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 36 ASP 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 76 ILE Chi-restraints excluded: chain l residue 83 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 125 GLN Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 77 LEU Chi-restraints excluded: chain r residue 55 LYS Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 45 ILE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 42 ASN Chi-restraints excluded: chain t residue 45 ASN Chi-restraints excluded: chain t residue 49 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 370 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 340 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 89 GLN ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 35 GLN d 70 ASN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 HIS ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN l 90 HIS ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** 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 ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 55771 Z= 0.213 Angle : 0.639 8.439 82915 Z= 0.329 Chirality : 0.036 0.276 10533 Planarity : 0.005 0.076 4786 Dihedral : 23.644 179.775 26585 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.50 % Allowed : 19.63 % Favored : 75.87 % 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: -2.60 (0.17), residues: 2269 helix: -0.35 (0.18), residues: 813 sheet: -2.38 (0.24), residues: 370 loop : -2.58 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 200 HIS 0.018 0.002 HIS l 90 PHE 0.023 0.002 PHE h 45 TYR 0.023 0.002 TYR q 30 ARG 0.011 0.001 ARG o 7 *********************** 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 288 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 199 time to evaluate : 3.307 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: b 73 LYS cc_start: 0.6658 (tttt) cc_final: 0.6447 (tttm) REVERT: b 154 MET cc_start: 0.7037 (tpt) cc_final: 0.6520 (tpt) REVERT: e 25 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7469 (p) REVERT: e 145 GLN cc_start: 0.8540 (mm110) cc_final: 0.8237 (mm110) REVERT: f 88 ARG cc_start: 0.5738 (mmm160) cc_final: 0.5525 (mmm160) REVERT: f 90 MET cc_start: 0.5041 (mmt) cc_final: 0.4599 (mmt) REVERT: g 70 MET cc_start: 0.6182 (ptm) cc_final: 0.5658 (mmt) REVERT: h 20 VAL cc_start: 0.7643 (p) cc_final: 0.7312 (m) REVERT: h 46 ILE cc_start: 0.7308 (mm) cc_final: 0.7050 (mm) REVERT: j 1 MET cc_start: 0.4798 (tmm) cc_final: 0.4262 (tmm) REVERT: j 73 LEU cc_start: 0.9017 (tp) cc_final: 0.8310 (pp) REVERT: j 88 MET cc_start: 0.6015 (ptp) cc_final: 0.5799 (ptp) REVERT: k 24 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6002 (mtp180) REVERT: k 87 LYS cc_start: 0.7455 (ptmm) cc_final: 0.6874 (mtmt) REVERT: o 17 VAL cc_start: 0.7512 (m) cc_final: 0.7083 (t) REVERT: o 41 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8597 (mm-30) REVERT: r 18 PHE cc_start: 0.3604 (p90) cc_final: 0.3327 (t80) REVERT: s 16 MET cc_start: 0.5884 (mmm) cc_final: 0.5557 (mmm) REVERT: s 26 GLU cc_start: 0.7929 (tt0) cc_final: 0.7641 (tm-30) REVERT: t 28 MET cc_start: 0.8327 (mmm) cc_final: 0.7927 (mmm) outliers start: 89 outliers final: 55 residues processed: 262 average time/residue: 0.6331 time to fit residues: 280.3165 Evaluate side-chains 237 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 180 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 91 TYR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 23 TYR Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 25 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 4 TYR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 67 SER Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain i residue 8 TYR Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 84 VAL 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 24 ARG Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 44 TRP 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 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 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 53 LEU Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain n residue 53 ILE Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 20 ASP Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain r residue 55 LYS Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 61 TYR Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 30 THR 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: 3.9990 chunk 257 optimal weight: 0.7980 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 364 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 326 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 70 ASN d 116 HIS e 149 ASN g 106 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 GLN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS o 9 ASN ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 5 ASN ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 55771 Z= 0.150 Angle : 0.552 8.450 82915 Z= 0.283 Chirality : 0.032 0.245 10533 Planarity : 0.005 0.059 4786 Dihedral : 23.323 177.527 26583 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.55 % Allowed : 20.49 % Favored : 74.96 % 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: -2.20 (0.17), residues: 2269 helix: 0.07 (0.18), residues: 815 sheet: -2.08 (0.25), residues: 361 loop : -2.47 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 200 HIS 0.012 0.001 HIS l 90 PHE 0.031 0.002 PHE k 61 TYR 0.021 0.001 TYR c 183 ARG 0.005 0.000 ARG q 39 *********************** 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 303 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 213 time to evaluate : 3.310 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: b 96 TRP cc_start: 0.6545 (t-100) cc_final: 0.6292 (t-100) REVERT: b 129 LEU cc_start: 0.5162 (OUTLIER) cc_final: 0.4910 (tp) REVERT: b 154 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6773 (tpt) REVERT: e 25 VAL cc_start: 0.7722 (m) cc_final: 0.7456 (p) REVERT: e 145 GLN cc_start: 0.8376 (mm110) cc_final: 0.8016 (mm110) REVERT: f 7 MET cc_start: 0.1567 (tmm) cc_final: 0.1344 (tmm) REVERT: f 88 ARG cc_start: 0.5439 (mmm160) cc_final: 0.5221 (mmm160) REVERT: f 90 MET cc_start: 0.4153 (mmt) cc_final: 0.3849 (mmt) REVERT: g 67 ASN cc_start: 0.6425 (OUTLIER) cc_final: 0.5546 (t0) REVERT: g 70 MET cc_start: 0.5877 (ptm) cc_final: 0.5425 (mmt) REVERT: i 116 LYS cc_start: 0.7103 (tttm) cc_final: 0.6848 (tmtt) REVERT: j 1 MET cc_start: 0.4827 (tmm) cc_final: 0.4374 (tmm) REVERT: k 24 ARG cc_start: 0.6812 (mtm-85) cc_final: 0.6354 (mtp180) REVERT: k 32 VAL cc_start: 0.6837 (OUTLIER) cc_final: 0.6013 (p) REVERT: k 87 LYS cc_start: 0.7594 (ptmm) cc_final: 0.7326 (pttt) REVERT: n 13 LYS cc_start: 0.6855 (mmmt) cc_final: 0.6454 (mttt) REVERT: o 17 VAL cc_start: 0.7151 (m) cc_final: 0.6662 (t) REVERT: o 28 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: o 41 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8612 (mm-30) REVERT: r 18 PHE cc_start: 0.4171 (p90) cc_final: 0.3892 (t80) REVERT: r 25 HIS cc_start: 0.4970 (OUTLIER) cc_final: 0.4707 (p-80) REVERT: t 72 ASP cc_start: 0.7920 (m-30) cc_final: 0.7641 (t0) outliers start: 90 outliers final: 47 residues processed: 281 average time/residue: 0.6267 time to fit residues: 294.4628 Evaluate side-chains 244 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 191 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 91 TYR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain c residue 23 TYR Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 189 ILE 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 48 LEU Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 44 TRP 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 52 THR Chi-restraints excluded: chain l residue 68 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 22 ILE Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 55 LYS Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 61 TYR Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 30 THR 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: 9.9990 chunk 206 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 327 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 b 225 GLN c 44 ASN d 70 ASN d 149 ASN e 146 ASN ** f 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 61 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 ASN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS o 9 ASN ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 55771 Z= 0.358 Angle : 0.874 14.132 82915 Z= 0.437 Chirality : 0.045 0.327 10533 Planarity : 0.007 0.069 4786 Dihedral : 24.031 178.588 26583 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 37.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.67 % Favored : 89.29 % Rotamer: Outliers : 6.58 % Allowed : 21.19 % Favored : 72.23 % 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: -2.82 (0.16), residues: 2269 helix: -0.73 (0.17), residues: 823 sheet: -2.14 (0.26), residues: 369 loop : -2.71 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP d 9 HIS 0.018 0.002 HIS l 90 PHE 0.022 0.003 PHE k 27 TYR 0.027 0.003 TYR j 58 ARG 0.010 0.001 ARG o 53 *********************** 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 329 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 199 time to evaluate : 3.375 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 90 PHE cc_start: 0.3493 (OUTLIER) cc_final: 0.2855 (p90) REVERT: b 152 ARG cc_start: 0.7057 (mtp180) cc_final: 0.6455 (mpt90) REVERT: b 170 ARG cc_start: 0.8859 (mmt-90) cc_final: 0.8540 (mmt-90) REVERT: b 217 MET cc_start: 0.5579 (mmm) cc_final: 0.5045 (ppp) REVERT: c 141 MET cc_start: 0.8581 (mmm) cc_final: 0.8362 (mmm) REVERT: c 172 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7685 (m) REVERT: c 180 ASP cc_start: 0.7935 (t70) cc_final: 0.7672 (t0) REVERT: e 145 GLN cc_start: 0.8279 (mm110) cc_final: 0.8021 (mm110) REVERT: f 1 MET cc_start: 0.6889 (ppp) cc_final: 0.6683 (ppp) REVERT: f 2 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.4491 (tpp80) REVERT: f 88 ARG cc_start: 0.5426 (mmm160) cc_final: 0.5142 (mmm160) REVERT: f 90 MET cc_start: 0.3069 (mmt) cc_final: 0.2184 (mpp) REVERT: g 67 ASN cc_start: 0.6306 (OUTLIER) cc_final: 0.4983 (m-40) REVERT: g 70 MET cc_start: 0.5775 (ptm) cc_final: 0.5395 (mmt) REVERT: k 24 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.7030 (mtm180) REVERT: r 70 MET cc_start: 0.0767 (OUTLIER) cc_final: 0.0527 (tpp) REVERT: s 14 HIS cc_start: 0.2086 (OUTLIER) cc_final: 0.1421 (t-90) REVERT: s 27 LYS cc_start: 0.3766 (mttt) cc_final: 0.1262 (pttp) REVERT: s 74 PHE cc_start: 0.5559 (OUTLIER) cc_final: 0.5205 (p90) REVERT: t 22 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8610 (tp) REVERT: t 28 MET cc_start: 0.8358 (mmm) cc_final: 0.7753 (mmm) outliers start: 130 outliers final: 81 residues processed: 301 average time/residue: 0.6415 time to fit residues: 322.7431 Evaluate side-chains 263 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 173 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 91 TYR Chi-restraints excluded: chain b residue 93 ASN 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 183 ILE 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 c residue 71 LYS Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 78 GLU 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 2 ARG 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 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 32 SER 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 24 ARG Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 83 ILE Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 115 LEU 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 50 ASP Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 44 SER Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 74 ILE Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 20 ASP Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 61 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 26 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 42 ASN Chi-restraints excluded: chain t residue 45 ASN 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: 1.9990 chunk 72 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 364 optimal weight: 0.4980 chunk 302 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 191 optimal weight: 0.1980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 75 GLN b 225 GLN d 40 GLN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 ASN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 77 GLN l 90 HIS ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 55771 Z= 0.183 Angle : 0.617 9.625 82915 Z= 0.317 Chirality : 0.035 0.281 10533 Planarity : 0.005 0.051 4786 Dihedral : 23.609 179.948 26581 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.21 % Allowed : 22.51 % Favored : 72.28 % 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: -2.40 (0.17), residues: 2269 helix: -0.25 (0.17), residues: 825 sheet: -2.13 (0.26), residues: 367 loop : -2.50 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 96 HIS 0.014 0.001 HIS l 90 PHE 0.028 0.002 PHE f 59 TYR 0.018 0.002 TYR q 30 ARG 0.010 0.001 ARG b 143 *********************** 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 298 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 195 time to evaluate : 3.269 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: b 89 GLN cc_start: 0.4489 (mm110) cc_final: 0.4158 (mp10) REVERT: b 90 PHE cc_start: 0.2813 (OUTLIER) cc_final: 0.2332 (p90) REVERT: b 96 TRP cc_start: 0.6860 (t-100) cc_final: 0.6576 (t-100) REVERT: b 170 ARG cc_start: 0.8658 (mmt-90) cc_final: 0.8367 (mmt-90) REVERT: b 217 MET cc_start: 0.5695 (mmm) cc_final: 0.5335 (ppp) REVERT: d 59 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.5932 (m-80) REVERT: e 136 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7513 (tmm) REVERT: f 88 ARG cc_start: 0.4969 (mmm160) cc_final: 0.4643 (mmm160) REVERT: f 90 MET cc_start: 0.3160 (mmt) cc_final: 0.2397 (mpp) REVERT: g 67 ASN cc_start: 0.6377 (OUTLIER) cc_final: 0.5300 (m-40) REVERT: g 70 MET cc_start: 0.5950 (ptm) cc_final: 0.5487 (mmt) REVERT: k 40 ASN cc_start: 0.6953 (m-40) cc_final: 0.6638 (t0) REVERT: k 44 TRP cc_start: 0.4019 (OUTLIER) cc_final: 0.3631 (p-90) REVERT: k 75 MET cc_start: 0.5687 (mmt) cc_final: 0.5342 (mmp) REVERT: o 28 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: r 70 MET cc_start: 0.0968 (OUTLIER) cc_final: 0.0688 (tpp) REVERT: s 26 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7458 (tm-30) REVERT: s 27 LYS cc_start: 0.3820 (mttt) cc_final: 0.1491 (pttp) REVERT: s 74 PHE cc_start: 0.5239 (OUTLIER) cc_final: 0.4889 (p90) REVERT: t 28 MET cc_start: 0.8447 (mmm) cc_final: 0.7489 (mmm) REVERT: t 72 ASP cc_start: 0.7642 (m-30) cc_final: 0.7378 (t0) outliers start: 103 outliers final: 69 residues processed: 279 average time/residue: 0.6496 time to fit residues: 303.0058 Evaluate side-chains 252 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 175 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 90 PHE 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 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 b residue 225 GLN Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 23 TYR Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 59 TYR 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 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 67 SER Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 32 SER 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 30 THR Chi-restraints excluded: chain k residue 44 TRP 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 30 SER 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 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 50 ASP 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 22 THR Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain n residue 53 ILE 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 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 52 ASN Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 61 TYR Chi-restraints excluded: chain s residue 74 PHE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 42 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 307 optimal weight: 0.7980 chunk 203 optimal weight: 9.9990 chunk 363 optimal weight: 30.0000 chunk 227 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 93 ASN b 225 GLN d 40 GLN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** 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: 0.7318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 55771 Z= 0.182 Angle : 0.602 10.812 82915 Z= 0.308 Chirality : 0.034 0.273 10533 Planarity : 0.005 0.056 4786 Dihedral : 23.452 179.725 26579 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.68 % Favored : 91.27 % Rotamer: Outliers : 5.56 % Allowed : 22.41 % Favored : 72.03 % 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: -2.26 (0.17), residues: 2269 helix: -0.02 (0.18), residues: 822 sheet: -2.02 (0.27), residues: 361 loop : -2.52 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP s 34 HIS 0.033 0.001 HIS l 90 PHE 0.020 0.002 PHE h 45 TYR 0.019 0.002 TYR c 183 ARG 0.006 0.001 ARG b 143 *********************** 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 298 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 188 time to evaluate : 3.231 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 83 GLU cc_start: 0.4970 (OUTLIER) cc_final: 0.4507 (pm20) REVERT: b 89 GLN cc_start: 0.4945 (mm110) cc_final: 0.4637 (mp10) REVERT: b 90 PHE cc_start: 0.2596 (OUTLIER) cc_final: 0.2194 (p90) REVERT: b 152 ARG cc_start: 0.7475 (mtp180) cc_final: 0.6574 (mpt90) REVERT: b 217 MET cc_start: 0.5770 (mmm) cc_final: 0.5363 (ppp) REVERT: d 40 GLN cc_start: 0.5997 (OUTLIER) cc_final: 0.5668 (pp30) REVERT: d 59 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.6018 (m-80) REVERT: e 136 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7525 (tmm) REVERT: e 145 GLN cc_start: 0.8284 (mm110) cc_final: 0.8038 (mm110) REVERT: f 88 ARG cc_start: 0.4903 (mmm160) cc_final: 0.4186 (mmm160) REVERT: f 90 MET cc_start: 0.3236 (mmt) cc_final: 0.2730 (mpp) REVERT: g 67 ASN cc_start: 0.6204 (OUTLIER) cc_final: 0.5125 (m-40) REVERT: g 70 MET cc_start: 0.5749 (ptm) cc_final: 0.5293 (mmt) REVERT: g 136 LYS cc_start: 0.8175 (mttp) cc_final: 0.7965 (pttm) REVERT: j 1 MET cc_start: 0.5049 (tmm) cc_final: 0.4685 (tmm) REVERT: k 14 LYS cc_start: 0.2631 (OUTLIER) cc_final: 0.2353 (ptmm) REVERT: k 40 ASN cc_start: 0.6885 (m-40) cc_final: 0.6606 (t0) REVERT: k 75 MET cc_start: 0.5687 (mmt) cc_final: 0.5350 (mmp) REVERT: l 136 LYS cc_start: 0.6109 (mptt) cc_final: 0.5452 (mmtt) REVERT: o 28 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7177 (mp10) REVERT: o 48 LYS cc_start: 0.6125 (OUTLIER) cc_final: 0.5462 (tptp) REVERT: r 70 MET cc_start: 0.1207 (OUTLIER) cc_final: 0.0870 (tpp) REVERT: s 26 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7505 (tm-30) REVERT: s 27 LYS cc_start: 0.3765 (mttt) cc_final: 0.1570 (pttp) REVERT: s 74 PHE cc_start: 0.5209 (OUTLIER) cc_final: 0.4825 (p90) REVERT: t 28 MET cc_start: 0.8578 (mmm) cc_final: 0.7713 (mmm) outliers start: 110 outliers final: 73 residues processed: 274 average time/residue: 0.6537 time to fit residues: 298.6182 Evaluate side-chains 259 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 175 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 83 GLU 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 157 MET 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 23 TYR Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 59 TYR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 189 ILE 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 136 MET 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 48 LEU Chi-restraints excluded: chain f residue 67 SER Chi-restraints excluded: chain f residue 91 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 67 ASN Chi-restraints excluded: chain g residue 135 VAL 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 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 32 SER 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 14 LYS Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 44 TRP Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 30 SER 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 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 50 ASP 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 22 THR Chi-restraints excluded: chain n residue 37 PHE 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 48 LYS Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 51 LYS Chi-restraints excluded: chain p residue 69 ASP 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 52 ASN Chi-restraints excluded: chain q residue 53 ASN Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain r residue 70 MET 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 30 THR Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.0980 chunk 145 optimal weight: 20.0000 chunk 217 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 247 optimal weight: 0.3980 chunk 179 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 93 ASN f 53 ASN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS m 31 GLN ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 14 HIS ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.8336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 55771 Z= 0.284 Angle : 0.742 12.983 82915 Z= 0.375 Chirality : 0.040 0.308 10533 Planarity : 0.006 0.133 4786 Dihedral : 23.745 179.914 26579 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.84 % Favored : 89.11 % Rotamer: Outliers : 5.46 % Allowed : 22.91 % Favored : 71.62 % 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: -0.34 (0.17), residues: 812 sheet: -2.15 (0.26), residues: 382 loop : -2.65 (0.17), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP s 34 HIS 0.017 0.002 HIS l 90 PHE 0.019 0.002 PHE k 27 TYR 0.024 0.002 TYR q 30 ARG 0.009 0.001 ARG b 170 *********************** 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 296 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 188 time to evaluate : 2.878 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 83 GLU cc_start: 0.4977 (OUTLIER) cc_final: 0.4448 (pm20) REVERT: b 90 PHE cc_start: 0.2629 (OUTLIER) cc_final: 0.1846 (p90) REVERT: b 152 ARG cc_start: 0.6884 (mtp180) cc_final: 0.6360 (mpt90) REVERT: b 154 MET cc_start: 0.7039 (tpt) cc_final: 0.6533 (tpt) REVERT: b 217 MET cc_start: 0.5971 (mmm) cc_final: 0.5508 (ppp) REVERT: c 15 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8549 (mm) REVERT: d 59 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.5597 (m-80) REVERT: e 136 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7536 (tmm) REVERT: f 88 ARG cc_start: 0.4470 (mmm160) cc_final: 0.3873 (mmm160) REVERT: f 90 MET cc_start: 0.2083 (mmt) cc_final: 0.1500 (mpp) REVERT: g 67 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.5049 (m-40) REVERT: g 70 MET cc_start: 0.5930 (ptm) cc_final: 0.5461 (mmt) REVERT: g 116 MET cc_start: 0.2591 (mmp) cc_final: 0.2295 (mmp) REVERT: g 136 LYS cc_start: 0.8318 (mttp) cc_final: 0.7930 (tmmt) REVERT: h 19 MET cc_start: 0.6934 (ppp) cc_final: 0.6681 (ppp) REVERT: j 58 TYR cc_start: 0.6030 (m-10) cc_final: 0.5743 (m-10) REVERT: l 136 LYS cc_start: 0.6160 (mptt) cc_final: 0.5912 (mmtt) REVERT: q 4 ARG cc_start: 0.5385 (ptm160) cc_final: 0.5172 (ptm160) REVERT: r 25 HIS cc_start: 0.6194 (OUTLIER) cc_final: 0.5632 (m90) REVERT: s 14 HIS cc_start: 0.2203 (OUTLIER) cc_final: 0.1539 (t70) REVERT: s 26 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7488 (tm-30) REVERT: s 27 LYS cc_start: 0.4290 (mttt) cc_final: 0.1812 (pttp) REVERT: s 74 PHE cc_start: 0.5262 (OUTLIER) cc_final: 0.4985 (p90) REVERT: t 28 MET cc_start: 0.8545 (mmm) cc_final: 0.8123 (mmm) outliers start: 108 outliers final: 76 residues processed: 275 average time/residue: 0.6537 time to fit residues: 299.6025 Evaluate side-chains 259 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 174 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 61 SER Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 135 VAL 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 15 ILE Chi-restraints excluded: chain c residue 23 TYR Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain d residue 59 TYR 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 24 VAL Chi-restraints excluded: chain e residue 46 VAL 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 6 VAL Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 135 VAL 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 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 32 SER 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 30 THR Chi-restraints excluded: chain k residue 84 VAL 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 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 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 50 ASP Chi-restraints excluded: chain m residue 60 VAL 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 o residue 4 SER Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 20 ASP 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 25 HIS Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 64 ILE 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 30 THR 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: 1.9990 chunk 348 optimal weight: 0.9980 chunk 317 optimal weight: 6.9990 chunk 338 optimal weight: 0.9980 chunk 203 optimal weight: 0.0770 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 305 optimal weight: 4.9990 chunk 320 optimal weight: 5.9990 chunk 337 optimal weight: 2.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 118 ASN c 175 HIS ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 14 HIS t 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.8408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 55771 Z= 0.152 Angle : 0.591 10.314 82915 Z= 0.301 Chirality : 0.033 0.273 10533 Planarity : 0.005 0.049 4786 Dihedral : 23.428 178.998 26579 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.49 % Allowed : 24.63 % Favored : 71.88 % 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: -2.28 (0.17), residues: 2269 helix: -0.13 (0.18), residues: 832 sheet: -2.00 (0.26), residues: 377 loop : -2.49 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP k 44 HIS 0.010 0.001 HIS s 14 PHE 0.026 0.002 PHE k 61 TYR 0.017 0.002 TYR l 108 ARG 0.005 0.001 ARG b 170 *********************** 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 258 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 189 time to evaluate : 3.274 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: 0.2481 (OUTLIER) cc_final: 0.1809 (p90) REVERT: b 152 ARG cc_start: 0.7424 (mtp180) cc_final: 0.6651 (mpt90) REVERT: b 154 MET cc_start: 0.7391 (tpt) cc_final: 0.6962 (tpt) REVERT: b 217 MET cc_start: 0.5994 (mmm) cc_final: 0.5656 (ppp) REVERT: c 15 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8314 (mm) REVERT: c 84 GLU cc_start: 0.7443 (pm20) cc_final: 0.6758 (pm20) REVERT: e 136 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7365 (tmm) REVERT: f 7 MET cc_start: 0.2471 (tmm) cc_final: 0.2021 (tmm) REVERT: f 90 MET cc_start: 0.2097 (mmt) cc_final: 0.1447 (mpp) REVERT: g 67 ASN cc_start: 0.6187 (OUTLIER) cc_final: 0.5166 (m-40) REVERT: g 70 MET cc_start: 0.5968 (ptm) cc_final: 0.5519 (mmt) REVERT: g 116 MET cc_start: 0.2141 (mmp) cc_final: 0.1855 (mmp) REVERT: h 19 MET cc_start: 0.6792 (ppp) cc_final: 0.6412 (ppp) REVERT: j 1 MET cc_start: 0.4929 (tmm) cc_final: 0.4530 (tmm) REVERT: j 32 SER cc_start: 0.2384 (OUTLIER) cc_final: 0.1869 (m) REVERT: j 68 ARG cc_start: 0.5059 (ttp80) cc_final: 0.4711 (ttp80) REVERT: k 75 MET cc_start: 0.5947 (mmt) cc_final: 0.5666 (mmp) REVERT: s 14 HIS cc_start: 0.1805 (OUTLIER) cc_final: 0.1286 (t-170) REVERT: s 26 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7446 (tm-30) REVERT: s 27 LYS cc_start: 0.3962 (mttt) cc_final: 0.1749 (pttp) REVERT: t 28 MET cc_start: 0.8467 (mmm) cc_final: 0.8026 (mmm) outliers start: 69 outliers final: 50 residues processed: 242 average time/residue: 0.6655 time to fit residues: 270.4831 Evaluate side-chains 233 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 177 time to evaluate : 3.383 ------------------------------------------------------------------------------- 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 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 c residue 15 ILE Chi-restraints excluded: chain c residue 23 TYR Chi-restraints excluded: chain c residue 118 ASN Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 46 VAL 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 6 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 67 ASN 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 i residue 67 VAL Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 36 VAL 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 84 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 24 LEU 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 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 60 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain q residue 20 ASP 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 r residue 75 TYR Chi-restraints excluded: chain s residue 14 HIS 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 222 optimal weight: 1.9990 chunk 358 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 169 optimal weight: 0.0980 chunk 248 optimal weight: 2.9990 chunk 375 optimal weight: 0.8980 chunk 345 optimal weight: 0.5980 chunk 299 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN g 67 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS m 31 GLN o 9 ASN ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 14 HIS t 21 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.8535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 55771 Z= 0.149 Angle : 0.579 11.344 82915 Z= 0.296 Chirality : 0.032 0.255 10533 Planarity : 0.004 0.050 4786 Dihedral : 23.292 179.056 26579 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.51 % Favored : 91.45 % Rotamer: Outliers : 2.88 % Allowed : 25.29 % Favored : 71.83 % 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: -2.27 (0.17), residues: 2269 helix: -0.13 (0.18), residues: 826 sheet: -1.98 (0.26), residues: 386 loop : -2.46 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP s 34 HIS 0.017 0.001 HIS s 14 PHE 0.047 0.002 PHE d 86 TYR 0.020 0.002 TYR g 107 ARG 0.008 0.000 ARG b 22 ********************** 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 240 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 183 time to evaluate : 3.239 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 90 PHE cc_start: 0.2695 (OUTLIER) cc_final: 0.1596 (p90) REVERT: b 152 ARG cc_start: 0.7396 (mtp180) cc_final: 0.6634 (mpt90) REVERT: b 154 MET cc_start: 0.7500 (tpt) cc_final: 0.6686 (tpt) REVERT: b 217 MET cc_start: 0.5988 (mmm) cc_final: 0.5619 (ppp) REVERT: b 219 ASP cc_start: 0.8571 (p0) cc_final: 0.8148 (m-30) REVERT: c 15 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8345 (mm) REVERT: e 136 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7387 (tmm) REVERT: f 7 MET cc_start: 0.2529 (tmm) cc_final: 0.2042 (tmm) REVERT: f 90 MET cc_start: 0.1899 (mmt) cc_final: 0.1197 (mpp) REVERT: g 70 MET cc_start: 0.6033 (ptm) cc_final: 0.5597 (mmt) REVERT: g 116 MET cc_start: 0.2166 (mmp) cc_final: 0.1874 (mmp) REVERT: g 136 LYS cc_start: 0.6020 (pttm) cc_final: 0.5812 (pttp) REVERT: h 19 MET cc_start: 0.6842 (ppp) cc_final: 0.6487 (ppp) REVERT: h 46 ILE cc_start: 0.6488 (mt) cc_final: 0.6250 (mm) REVERT: i 124 ARG cc_start: 0.2037 (mtt180) cc_final: 0.0779 (mtt180) REVERT: j 1 MET cc_start: 0.5209 (tmm) cc_final: 0.4753 (tmm) REVERT: j 27 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6690 (mm-30) REVERT: j 32 SER cc_start: 0.2623 (OUTLIER) cc_final: 0.2194 (m) REVERT: k 40 ASN cc_start: 0.7451 (m-40) cc_final: 0.7121 (t0) REVERT: k 75 MET cc_start: 0.6073 (mmt) cc_final: 0.5764 (mmp) REVERT: s 26 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7431 (tm-30) REVERT: s 27 LYS cc_start: 0.4265 (mttt) cc_final: 0.2000 (pttp) REVERT: t 28 MET cc_start: 0.8481 (mmm) cc_final: 0.8039 (mmm) outliers start: 57 outliers final: 46 residues processed: 226 average time/residue: 0.6485 time to fit residues: 245.2017 Evaluate side-chains 227 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 176 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 61 SER Chi-restraints excluded: chain b residue 90 PHE 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 15 ILE Chi-restraints excluded: chain c residue 23 TYR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 46 VAL 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 6 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain g residue 12 VAL 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 i residue 67 VAL Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 36 VAL 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 84 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 24 LEU 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 90 HIS 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 60 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 37 PHE Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain q residue 20 ASP 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 r residue 75 TYR 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 237 optimal weight: 0.9990 chunk 318 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 275 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 299 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 307 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS m 31 GLN o 9 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.066637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.054683 restraints weight = 454793.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.056035 restraints weight = 229681.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.056796 restraints weight = 157514.123| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.9338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 55771 Z= 0.346 Angle : 0.809 11.265 82915 Z= 0.408 Chirality : 0.043 0.308 10533 Planarity : 0.006 0.057 4786 Dihedral : 23.789 179.990 26579 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 36.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.86 % Favored : 88.10 % Rotamer: Outliers : 3.84 % Allowed : 24.43 % Favored : 71.72 % 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: -2.67 (0.17), residues: 2269 helix: -0.57 (0.17), residues: 812 sheet: -2.00 (0.26), residues: 380 loop : -2.67 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP d 9 HIS 0.053 0.003 HIS l 90 PHE 0.035 0.003 PHE k 61 TYR 0.025 0.003 TYR j 58 ARG 0.012 0.001 ARG b 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8100.06 seconds wall clock time: 150 minutes 57.43 seconds (9057.43 seconds total)