Starting phenix.real_space_refine on Tue Feb 13 03:28:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2024/5zeu_6923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2024/5zeu_6923.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/5zeu_6923/02_2024/5zeu_6923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2024/5zeu_6923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2024/5zeu_6923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2024/5zeu_6923.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= 0.002 sd= 0.015 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 1583 5.49 5 S 47 5.16 5 C 27003 2.51 5 N 9896 2.21 5 O 14425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c ARG 58": "NH1" <-> "NH2" Residue "c ARG 60": "NH1" <-> "NH2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "c ARG 71": "NH1" <-> "NH2" Residue "c ARG 78": "NH1" <-> "NH2" Residue "c ARG 79": "NH1" <-> "NH2" Residue "c ARG 87": "NH1" <-> "NH2" Residue "c GLU 109": "OE1" <-> "OE2" Residue "c ARG 126": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 134": "NH1" <-> "NH2" Residue "c ARG 150": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "c ARG 172": "NH1" <-> "NH2" Residue "c ARG 179": "NH1" <-> "NH2" Residue "c ARG 195": "NH1" <-> "NH2" Residue "e ARG 54": "NH1" <-> "NH2" Residue "e ARG 55": "NH1" <-> "NH2" Residue "e ARG 98": "NH1" <-> "NH2" Residue "e ARG 122": "NH1" <-> "NH2" Residue "e ARG 137": "NH1" <-> "NH2" Residue "e ARG 174": "NH1" <-> "NH2" Residue "e ARG 181": "NH1" <-> "NH2" Residue "e GLU 187": "OE1" <-> "OE2" Residue "e ARG 198": "NH1" <-> "NH2" Residue "g ARG 51": "NH1" <-> "NH2" Residue "g ARG 64": "NH1" <-> "NH2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g ARG 92": "NH1" <-> "NH2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ARG 109": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 112": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 137": "NH1" <-> "NH2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "g ARG 149": "NH1" <-> "NH2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h ARG 15": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 79": "NH1" <-> "NH2" Residue "h ARG 86": "NH1" <-> "NH2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "h TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 31": "NH1" <-> "NH2" Residue "i ARG 38": "NH1" <-> "NH2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "i ARG 100": "NH1" <-> "NH2" Residue "i ARG 105": "NH1" <-> "NH2" Residue "i ARG 115": "NH1" <-> "NH2" Residue "i ARG 126": "NH1" <-> "NH2" Residue "i TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 142": "NH1" <-> "NH2" Residue "i ARG 150": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 31": "NH1" <-> "NH2" Residue "j ARG 62": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ARG 89": "NH1" <-> "NH2" Residue "k ARG 65": "NH1" <-> "NH2" Residue "k ARG 81": "NH1" <-> "NH2" Residue "k ARG 102": "NH1" <-> "NH2" Residue "k ARG 107": "NH1" <-> "NH2" Residue "k ARG 131": "NH1" <-> "NH2" Residue "k ARG 135": "NH1" <-> "NH2" Residue "k ARG 137": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ARG 31": "NH1" <-> "NH2" Residue "l TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 54": "NH1" <-> "NH2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ARG 86": "NH1" <-> "NH2" Residue "l ARG 94": "NH1" <-> "NH2" Residue "l ARG 99": "NH1" <-> "NH2" Residue "l ARG 110": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "l ARG 116": "NH1" <-> "NH2" Residue "o ARG 35": "NH1" <-> "NH2" Residue "o ARG 53": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ARG 62": "NH1" <-> "NH2" Residue "o ARG 63": "NH1" <-> "NH2" Residue "o ARG 64": "NH1" <-> "NH2" Residue "o ARG 65": "NH1" <-> "NH2" Residue "o ARG 77": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 20": "NH1" <-> "NH2" Residue "q ARG 43": "NH1" <-> "NH2" Residue "q ARG 73": "NH1" <-> "NH2" Residue "q ARG 80": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 39": "NH1" <-> "NH2" Residue "r ARG 49": "NH1" <-> "NH2" Residue "r ARG 52": "NH1" <-> "NH2" Residue "r ARG 72": "NH1" <-> "NH2" Residue "s ARG 36": "NH1" <-> "NH2" Residue "s ARG 37": "NH1" <-> "NH2" Residue "s ARG 55": "NH1" <-> "NH2" Residue "s ARG 78": "NH1" <-> "NH2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t ARG 16": "NH1" <-> "NH2" Residue "t ARG 20": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 33": "NH1" <-> "NH2" Residue "t ARG 36": "NH1" <-> "NH2" Residue "t ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 52954 Number of models: 1 Model: "" Number of chains: 22 Chain: "a" Number of atoms: 32341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1506, 32341 Classifications: {'RNA': 1506} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 85, 'rna3p_pur': 738, 'rna3p_pyr': 571} Link IDs: {'rna2p': 197, 'rna3p': 1308} Chain breaks: 1 Chain: "c" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1672 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 5, 'TRANS': 204} Chain: "e" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1433 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "g" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1240 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "h" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "i" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "j" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "k" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "o" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 709 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "q" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "r" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "s" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 630 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 655 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "v" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 34, 'rna3p_pyr': 35} Link IDs: {'rna2p': 7, 'rna3p': 69} Chain: "n" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "b" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "d" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "f" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "m" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "p" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "u" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 280 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Time building chain proxies: 20.46, per 1000 atoms: 0.39 Number of scatterers: 52954 At special positions: 0 Unit cell: (210, 204.75, 173.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 1583 15.00 O 14425 8.00 N 9896 7.00 C 27003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 57 " distance=2.03 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 Atom "ATOM 7331 O5' G a 350 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.26 Conformation dependent library (CDL) restraints added in 3.1 seconds 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4428 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 23 sheets defined 44.3% alpha, 16.0% beta 515 base pairs and 847 stacking pairs defined. Time for finding SS restraints: 19.26 Creating SS restraints... Processing helix chain 'c' and resid 27 through 42 Processing helix chain 'c' and resid 43 through 50 Processing helix chain 'c' and resid 82 through 94 removed outlier: 3.868A pdb=" N ILE c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 124 Processing helix chain 'c' and resid 128 through 135 Processing helix chain 'c' and resid 135 through 140 removed outlier: 4.364A pdb=" N SER c 139 " --> pdb=" O LYS c 135 " (cutoff:3.500A) Processing helix chain 'c' and resid 156 through 160 removed outlier: 3.527A pdb=" N GLY c 159 " --> pdb=" O ARG c 156 " (cutoff:3.500A) Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'e' and resid 133 through 143 Processing helix chain 'e' and resid 158 through 171 Processing helix chain 'e' and resid 174 through 182 Processing helix chain 'e' and resid 191 through 214 removed outlier: 3.604A pdb=" N ALA e 214 " --> pdb=" O ARG e 210 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.743A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.572A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 110 Processing helix chain 'g' and resid 116 through 130 Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.606A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 155 removed outlier: 3.740A pdb=" N HIS g 153 " --> pdb=" O ALA g 150 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR g 154 " --> pdb=" O PHE g 151 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG g 155 " --> pdb=" O ALA g 152 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 removed outlier: 3.730A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 97 through 101 Processing helix chain 'h' and resid 114 through 121 Processing helix chain 'i' and resid 54 through 59 Processing helix chain 'i' and resid 63 through 75 removed outlier: 3.575A pdb=" N LYS i 69 " --> pdb=" O GLN i 65 " (cutoff:3.500A) Proline residue: i 71 - end of helix removed outlier: 3.614A pdb=" N VAL i 75 " --> pdb=" O PRO i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 109 removed outlier: 3.748A pdb=" N GLN i 95 " --> pdb=" O GLY i 91 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 113 No H-bonds generated for 'chain 'i' and resid 111 through 113' Processing helix chain 'i' and resid 114 through 122 removed outlier: 3.825A pdb=" N ALA i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY i 122 " --> pdb=" O LEU i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.136A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 60 removed outlier: 3.558A pdb=" N GLY k 60 " --> pdb=" O SER k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 56 through 60' Processing helix chain 'k' and resid 62 through 67 removed outlier: 3.769A pdb=" N ARG k 65 " --> pdb=" O LYS k 62 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 85 Processing helix chain 'k' and resid 102 through 112 Processing helix chain 'l' and resid 4 through 10 Processing helix chain 'o' and resid 6 through 16 removed outlier: 3.657A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 Processing helix chain 'o' and resid 51 through 74 Processing helix chain 'o' and resid 74 through 86 Processing helix chain 'r' and resid 34 through 40 removed outlier: 3.698A pdb=" N LEU r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 Processing helix chain 'r' and resid 57 through 74 Processing helix chain 's' and resid 12 through 25 Processing helix chain 's' and resid 41 through 45 removed outlier: 3.598A pdb=" N PHE s 44 " --> pdb=" O ILE s 41 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 41 through 45' Processing helix chain 's' and resid 63 through 67 removed outlier: 3.828A pdb=" N VAL s 67 " --> pdb=" O GLU s 64 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 removed outlier: 3.623A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 40 removed outlier: 3.750A pdb=" N ILE t 11 " --> pdb=" O GLN t 7 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 Processing helix chain 't' and resid 68 through 86 removed outlier: 4.212A pdb=" N LYS t 85 " --> pdb=" O LEU t 81 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 10 Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.779A pdb=" N ALA n 20 " --> pdb=" O ALA n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 50 Processing helix chain 'b' and resid 5 through 12 removed outlier: 3.731A pdb=" N LEU b 9 " --> pdb=" O THR b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 28 Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.776A pdb=" N THR b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 87 Processing helix chain 'b' and resid 106 through 120 removed outlier: 3.820A pdb=" N ARG b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU b 111 " --> pdb=" O VAL b 107 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 3.514A pdb=" N LEU b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 155 removed outlier: 3.844A pdb=" N GLN b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 179 Processing helix chain 'b' and resid 192 through 196 removed outlier: 3.671A pdb=" N VAL b 195 " --> pdb=" O ASP b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 228 removed outlier: 4.130A pdb=" N ALA b 227 " --> pdb=" O GLU b 223 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG b 228 " --> pdb=" O GLY b 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 15 Processing helix chain 'd' and resid 24 through 29 Processing helix chain 'd' and resid 44 through 61 removed outlier: 3.885A pdb=" N GLN d 48 " --> pdb=" O SER d 44 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS d 53 " --> pdb=" O GLN d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 77 Processing helix chain 'd' and resid 80 through 91 Processing helix chain 'd' and resid 92 through 100 Processing helix chain 'd' and resid 105 through 115 Processing helix chain 'd' and resid 141 through 146 removed outlier: 3.818A pdb=" N ASN d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 156 Processing helix chain 'd' and resid 182 through 187 removed outlier: 3.782A pdb=" N ILE d 186 " --> pdb=" O GLU d 182 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP d 187 " --> pdb=" O ARG d 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 182 through 187' Processing helix chain 'd' and resid 192 through 200 removed outlier: 3.689A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 34 removed outlier: 3.863A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 4.625A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 82 removed outlier: 3.878A pdb=" N ASN f 80 " --> pdb=" O ASP f 76 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.784A pdb=" N ALA m 35 " --> pdb=" O ASN m 31 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 86 through 95 Processing helix chain 'm' and resid 107 through 112 removed outlier: 3.777A pdb=" N LYS m 111 " --> pdb=" O ALA m 107 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 62 Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 78 through 85 Processing helix chain 'p' and resid 101 through 114 Processing helix chain 'u' and resid 3 through 24 removed outlier: 4.686A pdb=" N LYS u 7 " --> pdb=" O SER u 3 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 33 Processing sheet with id=AA1, first strand: chain 'c' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'c' and resid 166 through 171 Processing sheet with id=AA3, first strand: chain 'e' and resid 37 through 50 removed outlier: 6.868A pdb=" N LEU e 61 " --> pdb=" O VAL e 41 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE e 43 " --> pdb=" O THR e 59 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR e 59 " --> pdb=" O ILE e 43 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG e 45 " --> pdb=" O SER e 57 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER e 57 " --> pdb=" O ARG e 45 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER e 47 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG e 55 " --> pdb=" O SER e 47 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL e 49 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY e 53 " --> pdb=" O VAL e 49 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL e 64 " --> pdb=" O GLY e 72 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET e 70 " --> pdb=" O ASP e 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 110 through 114 Processing sheet with id=AA5, first strand: chain 'g' and resid 73 through 75 Processing sheet with id=AA6, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.741A pdb=" N ASP h 48 " --> pdb=" O GLN h 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 103 through 104 Processing sheet with id=AA8, first strand: chain 'i' and resid 27 through 31 removed outlier: 5.740A pdb=" N ASN i 49 " --> pdb=" O ALA i 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'j' and resid 97 through 101 removed outlier: 4.122A pdb=" N SER j 35 " --> pdb=" O LEU j 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 40 through 46 removed outlier: 4.088A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR j 44 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR j 69 " --> pdb=" O THR j 44 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS j 46 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N MET j 67 " --> pdb=" O LYS j 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'n' and resid 56 through 58 Processing sheet with id=AB3, first strand: chain 'k' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'l' and resid 39 through 40 removed outlier: 4.538A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'q' and resid 52 through 62 removed outlier: 3.591A pdb=" N LYS q 44 " --> pdb=" O ILE q 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'q' and resid 77 through 78 Processing sheet with id=AB7, first strand: chain 's' and resid 31 through 33 removed outlier: 6.383A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR s 33 " --> pdb=" O HIS s 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 31 through 35 removed outlier: 6.775A pdb=" N ILE b 40 " --> pdb=" O PHE b 32 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP b 34 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE b 38 " --> pdb=" O ASP b 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 91 through 92 removed outlier: 8.022A pdb=" N VAL b 92 " --> pdb=" O VAL b 67 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE b 69 " --> pdb=" O VAL b 92 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU b 68 " --> pdb=" O TRP b 162 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL b 183 " --> pdb=" O TYR b 198 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE b 200 " --> pdb=" O VAL b 183 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA b 185 " --> pdb=" O ILE b 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 123 through 124 Processing sheet with id=AC2, first strand: chain 'f' and resid 39 through 40 removed outlier: 5.835A pdb=" N TYR f 60 " --> pdb=" O GLY f 44 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY f 44 " --> pdb=" O TYR f 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 39 through 40 removed outlier: 6.757A pdb=" N MET f 7 " --> pdb=" O THR f 88 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR f 88 " --> pdb=" O MET f 7 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE f 9 " --> pdb=" O LEU f 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 35 through 36 removed outlier: 7.081A pdb=" N VAL p 3 " --> pdb=" O GLN p 65 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 38 through 40 873 hydrogen bonds defined for protein. 2508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1308 hydrogen bonds 2066 hydrogen bond angles 0 basepair planarities 515 basepair parallelities 847 stacking parallelities Total time for adding SS restraints: 34.82 Time building geometry restraints manager: 21.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5814 1.32 - 1.45: 24462 1.45 - 1.57: 23779 1.57 - 1.70: 3158 1.70 - 1.83: 80 Bond restraints: 57293 Sorted by residual: bond pdb=" C LEU h 94 " pdb=" N PRO h 95 " ideal model delta sigma weight residual 1.332 1.386 -0.054 1.12e-02 7.97e+03 2.32e+01 bond pdb=" C GLY q 6 " pdb=" N PRO q 7 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.32e-02 5.74e+03 1.89e+01 bond pdb=" N PRO q 7 " pdb=" CD PRO q 7 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.75e+01 bond pdb=" N PRO c 108 " pdb=" CD PRO c 108 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO e 191 " pdb=" CD PRO e 191 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 ... (remaining 57288 not shown) Histogram of bond angle deviations from ideal: 85.08 - 96.04: 3 96.04 - 107.00: 10996 107.00 - 117.96: 42686 117.96 - 128.92: 29692 128.92 - 139.88: 1853 Bond angle restraints: 85230 Sorted by residual: angle pdb=" N LEU h 94 " pdb=" CA LEU h 94 " pdb=" C LEU h 94 " ideal model delta sigma weight residual 109.04 85.08 23.96 1.52e+00 4.33e-01 2.48e+02 angle pdb=" C PRO d 189 " pdb=" N LEU d 190 " pdb=" CA LEU d 190 " ideal model delta sigma weight residual 121.31 135.04 -13.73 1.49e+00 4.50e-01 8.49e+01 angle pdb=" C3' U a1482 " pdb=" O3' U a1482 " pdb=" P A a1483 " ideal model delta sigma weight residual 120.20 131.14 -10.94 1.50e+00 4.44e-01 5.32e+01 angle pdb=" N GLU k 115 " pdb=" CA GLU k 115 " pdb=" C GLU k 115 " ideal model delta sigma weight residual 109.07 119.71 -10.64 1.61e+00 3.86e-01 4.37e+01 angle pdb=" N SER o 24 " pdb=" CA SER o 24 " pdb=" C SER o 24 " ideal model delta sigma weight residual 109.83 101.77 8.06 1.27e+00 6.20e-01 4.03e+01 ... (remaining 85225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 32432 35.62 - 71.23: 4048 71.23 - 106.85: 483 106.85 - 142.46: 18 142.46 - 178.08: 21 Dihedral angle restraints: 37002 sinusoidal: 30123 harmonic: 6879 Sorted by residual: dihedral pdb=" CA ARG h 55 " pdb=" C ARG h 55 " pdb=" N VAL h 56 " pdb=" CA VAL h 56 " ideal model delta harmonic sigma weight residual -180.00 -105.67 -74.33 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" CA PRO c 144 " pdb=" C PRO c 144 " pdb=" N ASN c 145 " pdb=" CA ASN c 145 " ideal model delta harmonic sigma weight residual -180.00 -115.02 -64.98 0 5.00e+00 4.00e-02 1.69e+02 dihedral pdb=" CA LYS j 59 " pdb=" C LYS j 59 " pdb=" N ASP j 60 " pdb=" CA ASP j 60 " ideal model delta harmonic sigma weight residual 180.00 120.85 59.15 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 36999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 10473 0.125 - 0.250: 317 0.250 - 0.375: 12 0.375 - 0.500: 3 0.500 - 0.625: 2 Chirality restraints: 10807 Sorted by residual: chirality pdb=" C3' U a1482 " pdb=" C4' U a1482 " pdb=" O3' U a1482 " pdb=" C2' U a1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" CB VAL d 188 " pdb=" CA VAL d 188 " pdb=" CG1 VAL d 188 " pdb=" CG2 VAL d 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" C1' G a 713 " pdb=" O4' G a 713 " pdb=" C2' G a 713 " pdb=" N9 G a 713 " both_signs ideal model delta sigma weight residual False 2.46 2.05 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 10804 not shown) Planarity restraints: 4930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G a 953 " 0.049 2.00e-02 2.50e+03 2.42e-02 1.75e+01 pdb=" N9 G a 953 " -0.066 2.00e-02 2.50e+03 pdb=" C8 G a 953 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G a 953 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G a 953 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G a 953 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G a 953 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G a 953 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G a 953 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G a 953 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G a 953 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G a 953 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL d 188 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO d 189 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO d 189 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO d 189 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U a 110 " -0.050 2.00e-02 2.50e+03 2.49e-02 1.40e+01 pdb=" N1 U a 110 " 0.046 2.00e-02 2.50e+03 pdb=" C2 U a 110 " 0.019 2.00e-02 2.50e+03 pdb=" O2 U a 110 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U a 110 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U a 110 " -0.009 2.00e-02 2.50e+03 pdb=" O4 U a 110 " -0.018 2.00e-02 2.50e+03 pdb=" C5 U a 110 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U a 110 " 0.013 2.00e-02 2.50e+03 ... (remaining 4927 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 52 1.85 - 2.61: 1421 2.61 - 3.37: 62246 3.37 - 4.14: 169220 4.14 - 4.90: 239393 Nonbonded interactions: 472332 Sorted by model distance: nonbonded pdb=" O GLU c 109 " pdb=" OE1 GLN c 143 " model vdw 1.086 3.040 nonbonded pdb=" O2' G a1097 " pdb=" NH1 ARG i 126 " model vdw 1.088 2.520 nonbonded pdb=" OP1 G a 998 " pdb=" NE2 HIS s 14 " model vdw 1.090 2.520 nonbonded pdb=" C2 A a 940 " pdb=" NE ARG s 55 " model vdw 1.123 3.420 nonbonded pdb=" NE ARG e 17 " pdb=" CD1 ILE e 85 " model vdw 1.155 3.540 ... (remaining 472327 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 13.910 Check model and map are aligned: 0.570 Set scattering table: 0.380 Process input model: 134.410 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.007 0.079 57293 Z= 0.428 Angle : 1.111 23.957 85230 Z= 0.583 Chirality : 0.052 0.625 10807 Planarity : 0.007 0.096 4930 Dihedral : 23.804 178.080 32571 Min Nonbonded Distance : 1.086 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 1.10 % Allowed : 8.58 % Favored : 90.32 % Rotamer: Outliers : 1.40 % Allowed : 5.15 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.91 % Twisted General : 1.01 % 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: -4.22 (0.14), residues: 2366 helix: -3.08 (0.11), residues: 970 sheet: -1.90 (0.24), residues: 386 loop : -2.73 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP b 23 HIS 0.019 0.003 HIS k 127 PHE 0.041 0.003 PHE g 107 TYR 0.031 0.003 TYR l 117 ARG 0.024 0.001 ARG o 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 669 time to evaluate : 2.354 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: c 82 GLU cc_start: 0.5473 (tp30) cc_final: 0.5219 (mt-10) REVERT: c 151 VAL cc_start: 0.8824 (t) cc_final: 0.8619 (t) REVERT: e 130 VAL cc_start: 0.8867 (t) cc_final: 0.8518 (p) REVERT: h 93 ASN cc_start: 0.7257 (p0) cc_final: 0.7049 (p0) REVERT: i 86 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7307 (m170) REVERT: i 100 ARG cc_start: 0.7632 (ttm170) cc_final: 0.7427 (ttm170) REVERT: j 60 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5668 (p0) REVERT: l 39 THR cc_start: 0.7721 (m) cc_final: 0.7291 (p) REVERT: q 37 VAL cc_start: 0.9076 (t) cc_final: 0.8558 (p) REVERT: q 79 THR cc_start: 0.8448 (p) cc_final: 0.8140 (p) REVERT: n 8 HIS cc_start: 0.8411 (t70) cc_final: 0.8082 (t70) REVERT: b 6 MET cc_start: 0.4528 (mtp) cc_final: 0.3903 (tpp) REVERT: b 66 THR cc_start: 0.7180 (m) cc_final: 0.6837 (m) REVERT: b 148 LEU cc_start: 0.7609 (tp) cc_final: 0.7397 (tp) REVERT: b 168 LYS cc_start: 0.7107 (tptt) cc_final: 0.6621 (ttpp) REVERT: d 11 LYS cc_start: 0.6683 (mttt) cc_final: 0.6434 (mmmt) REVERT: d 25 SER cc_start: 0.7929 (m) cc_final: 0.7450 (t) REVERT: d 52 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7724 (tt0) REVERT: d 178 HIS cc_start: 0.6717 (m90) cc_final: 0.6056 (m-70) REVERT: d 193 GLN cc_start: 0.7246 (mm-40) cc_final: 0.7004 (mp10) REVERT: f 8 VAL cc_start: 0.9078 (t) cc_final: 0.8852 (p) REVERT: f 39 LYS cc_start: 0.8342 (tmmm) cc_final: 0.7944 (tmtt) REVERT: m 3 ARG cc_start: 0.6079 (tpt-90) cc_final: 0.5701 (mmm160) REVERT: m 4 LEU cc_start: 0.8751 (tp) cc_final: 0.8518 (tp) REVERT: m 23 TYR cc_start: 0.8064 (t80) cc_final: 0.7792 (t80) REVERT: m 88 GLN cc_start: 0.8515 (mt0) cc_final: 0.8286 (mt0) REVERT: m 94 ARG cc_start: 0.8106 (mmt180) cc_final: 0.7573 (mmt180) REVERT: p 15 ASN cc_start: 0.8379 (p0) cc_final: 0.8178 (p0) REVERT: p 19 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7568 (mtt90) REVERT: p 57 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8531 (mm110) REVERT: u 4 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7834 (t) REVERT: u 8 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.6137 (ttt-90) REVERT: u 10 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7203 (mmmt) outliers start: 28 outliers final: 11 residues processed: 689 average time/residue: 0.6428 time to fit residues: 676.7261 Evaluate side-chains 512 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 496 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 109 GLU Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 134 ARG Chi-restraints excluded: chain c residue 138 GLN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 182 ARG Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain i residue 86 HIS Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain u residue 4 VAL Chi-restraints excluded: chain u residue 8 ARG Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain u residue 30 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 328 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 304 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 226 optimal weight: 0.0470 chunk 353 optimal weight: 10.0000 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 101 ASN c 122 GLN c 145 ASN h 63 GLN h 117 GLN h 121 GLN i 61 ASN i 64 HIS ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 ASN k 31 HIS k 78 ASN l 6 GLN l 29 GLN ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 22 GLN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 GLN t 52 HIS b 167 ASN b 203 ASN d 95 ASN d 185 GLN f 80 ASN f 96 HIS p 17 GLN p 107 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 57293 Z= 0.227 Angle : 0.728 10.679 85230 Z= 0.370 Chirality : 0.040 0.279 10807 Planarity : 0.006 0.083 4930 Dihedral : 24.397 179.597 27786 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.11 % Favored : 91.50 % Rotamer: Outliers : 4.60 % Allowed : 13.86 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.26 % 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: -2.50 (0.15), residues: 2366 helix: -1.01 (0.15), residues: 1017 sheet: -1.32 (0.26), residues: 355 loop : -2.41 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP s 34 HIS 0.009 0.001 HIS k 127 PHE 0.029 0.002 PHE s 80 TYR 0.030 0.003 TYR r 32 ARG 0.011 0.001 ARG e 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 529 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 1 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.4454 (ptt) REVERT: c 113 GLN cc_start: 0.8287 (tp40) cc_final: 0.8013 (tp-100) REVERT: e 54 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: e 91 GLU cc_start: 0.6257 (tt0) cc_final: 0.5788 (tt0) REVERT: j 60 ASP cc_start: 0.5833 (OUTLIER) cc_final: 0.5447 (p0) REVERT: l 39 THR cc_start: 0.8002 (m) cc_final: 0.7640 (p) REVERT: q 79 THR cc_start: 0.8878 (p) cc_final: 0.8637 (p) REVERT: t 39 VAL cc_start: 0.7915 (m) cc_final: 0.7658 (m) REVERT: b 6 MET cc_start: 0.4619 (mtp) cc_final: 0.2538 (tmm) REVERT: b 152 ARG cc_start: 0.6192 (tpp80) cc_final: 0.5432 (mtt180) REVERT: b 168 LYS cc_start: 0.7043 (tptt) cc_final: 0.6536 (ttpp) REVERT: b 195 VAL cc_start: 0.5249 (OUTLIER) cc_final: 0.5038 (p) REVERT: d 36 HIS cc_start: 0.7098 (m-70) cc_final: 0.6894 (m90) REVERT: d 52 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7564 (tt0) REVERT: d 108 MET cc_start: 0.7206 (tpp) cc_final: 0.6920 (tpp) REVERT: d 178 HIS cc_start: 0.6480 (m90) cc_final: 0.5966 (m-70) REVERT: d 193 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7035 (mp10) REVERT: f 8 VAL cc_start: 0.9101 (t) cc_final: 0.8804 (p) REVERT: f 31 ARG cc_start: 0.5900 (mtt90) cc_final: 0.5693 (mtt180) REVERT: f 55 HIS cc_start: 0.7548 (m90) cc_final: 0.7321 (m90) REVERT: m 23 TYR cc_start: 0.8807 (t80) cc_final: 0.8568 (t80) REVERT: m 93 ARG cc_start: 0.7643 (mtt180) cc_final: 0.6432 (mmt-90) REVERT: m 94 ARG cc_start: 0.8187 (mmt180) cc_final: 0.7657 (mmt180) REVERT: p 15 ASN cc_start: 0.8397 (p0) cc_final: 0.7635 (p0) REVERT: p 57 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8511 (mm110) outliers start: 92 outliers final: 49 residues processed: 570 average time/residue: 0.5737 time to fit residues: 522.8240 Evaluate side-chains 515 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 463 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 142 CYS Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 128 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain q residue 76 LEU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 79 PHE Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain m residue 53 VAL Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 8 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 196 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 294 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 chunk 315 optimal weight: 0.0170 chunk 350 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 chunk 283 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 101 ASN g 68 ASN h 63 GLN h 121 GLN ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 7 GLN o 14 GLN r 56 ASN r 70 ASN d 178 HIS m 88 GLN ** p 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 57293 Z= 0.148 Angle : 0.601 10.706 85230 Z= 0.307 Chirality : 0.035 0.263 10807 Planarity : 0.005 0.084 4930 Dihedral : 24.088 179.115 27747 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.44 % Favored : 92.22 % Rotamer: Outliers : 4.10 % Allowed : 16.46 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2366 helix: -0.08 (0.16), residues: 1021 sheet: -1.13 (0.26), residues: 357 loop : -2.11 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP s 34 HIS 0.005 0.001 HIS c 68 PHE 0.018 0.002 PHE n 16 TYR 0.021 0.002 TYR n 21 ARG 0.020 0.001 ARG i 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 488 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 1 MET cc_start: 0.5133 (OUTLIER) cc_final: 0.4720 (ptt) REVERT: c 10 PHE cc_start: 0.8481 (t80) cc_final: 0.8113 (t80) REVERT: c 28 TYR cc_start: 0.7726 (t80) cc_final: 0.7412 (t80) REVERT: c 63 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6761 (p) REVERT: c 113 GLN cc_start: 0.8205 (tp40) cc_final: 0.7846 (tp-100) REVERT: c 126 ARG cc_start: 0.6479 (mtt180) cc_final: 0.6074 (mtm-85) REVERT: j 53 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8288 (ptt180) REVERT: j 60 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.5494 (p0) REVERT: l 39 THR cc_start: 0.7935 (m) cc_final: 0.7515 (p) REVERT: q 73 ARG cc_start: 0.6866 (mmm-85) cc_final: 0.6519 (ttp-170) REVERT: q 91 VAL cc_start: 0.7208 (OUTLIER) cc_final: 0.6121 (m) REVERT: q 92 GLU cc_start: 0.6695 (mp0) cc_final: 0.6190 (mp0) REVERT: t 49 GLU cc_start: 0.5734 (mm-30) cc_final: 0.5445 (mm-30) REVERT: b 6 MET cc_start: 0.4623 (mtp) cc_final: 0.2779 (tmm) REVERT: b 7 LYS cc_start: 0.5788 (mmtm) cc_final: 0.5479 (mppt) REVERT: b 168 LYS cc_start: 0.7031 (tptt) cc_final: 0.6502 (ttpp) REVERT: d 52 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7583 (tt0) REVERT: d 58 PHE cc_start: 0.7983 (m-80) cc_final: 0.7780 (m-10) REVERT: d 75 ASN cc_start: 0.8473 (m-40) cc_final: 0.8146 (m-40) REVERT: d 108 MET cc_start: 0.7217 (tpp) cc_final: 0.6897 (tpp) REVERT: f 8 VAL cc_start: 0.8984 (t) cc_final: 0.8638 (p) REVERT: f 66 LYS cc_start: 0.7946 (tttt) cc_final: 0.7734 (tttp) REVERT: m 23 TYR cc_start: 0.8567 (t80) cc_final: 0.8324 (t80) REVERT: m 43 MET cc_start: 0.8229 (ttt) cc_final: 0.7965 (ptm) REVERT: m 93 ARG cc_start: 0.7427 (mtt180) cc_final: 0.6144 (mmt-90) REVERT: m 94 ARG cc_start: 0.8200 (mmt180) cc_final: 0.7559 (mmt180) REVERT: p 15 ASN cc_start: 0.8411 (p0) cc_final: 0.7631 (p0) REVERT: p 57 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8489 (mm110) outliers start: 82 outliers final: 50 residues processed: 527 average time/residue: 0.5579 time to fit residues: 479.6415 Evaluate side-chains 487 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 432 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 90 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain g residue 128 SER Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain i residue 81 PHE Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 53 ARG Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain q residue 76 LEU Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 57 CYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 53 VAL Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 75 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 349 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 376 optimal weight: 0.4980 chunk 185 optimal weight: 0.9980 chunk 336 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 68 HIS c 101 ASN ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN h 63 GLN h 117 GLN j 56 HIS ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 7 GLN o 46 HIS r 60 HIS t 52 HIS t 74 ASN d 178 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 57293 Z= 0.240 Angle : 0.671 11.289 85230 Z= 0.338 Chirality : 0.037 0.275 10807 Planarity : 0.006 0.082 4930 Dihedral : 24.083 179.972 27747 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.26 % Favored : 90.45 % Rotamer: Outliers : 5.35 % Allowed : 17.11 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2366 helix: 0.31 (0.16), residues: 1001 sheet: -1.05 (0.26), residues: 352 loop : -1.92 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP k 53 HIS 0.012 0.001 HIS t 52 PHE 0.021 0.002 PHE s 80 TYR 0.025 0.002 TYR p 40 ARG 0.015 0.001 ARG c 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 460 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 PHE cc_start: 0.8528 (t80) cc_final: 0.8130 (t80) REVERT: c 28 TYR cc_start: 0.7797 (t80) cc_final: 0.7341 (t80) REVERT: c 55 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7465 (mt-10) REVERT: c 68 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6301 (m90) REVERT: j 53 ARG cc_start: 0.8490 (ptt180) cc_final: 0.8282 (ptt180) REVERT: l 39 THR cc_start: 0.8070 (m) cc_final: 0.7708 (p) REVERT: o 10 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6502 (tm-30) REVERT: r 79 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6377 (t80) REVERT: s 66 MET cc_start: 0.7916 (mmp) cc_final: 0.7404 (mmp) REVERT: b 6 MET cc_start: 0.4303 (mtp) cc_final: 0.3040 (tpp) REVERT: b 21 ARG cc_start: 0.6243 (mtt90) cc_final: 0.6013 (mmt90) REVERT: b 168 LYS cc_start: 0.7130 (tptt) cc_final: 0.6573 (ttpp) REVERT: b 195 VAL cc_start: 0.5253 (OUTLIER) cc_final: 0.4958 (p) REVERT: d 36 HIS cc_start: 0.7694 (m90) cc_final: 0.7439 (m90) REVERT: d 52 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7497 (tt0) REVERT: d 75 ASN cc_start: 0.8488 (t0) cc_final: 0.8102 (m-40) REVERT: d 98 TYR cc_start: 0.7332 (t80) cc_final: 0.7060 (t80) REVERT: d 108 MET cc_start: 0.7327 (tpp) cc_final: 0.6763 (tmm) REVERT: f 8 VAL cc_start: 0.9065 (t) cc_final: 0.8698 (p) REVERT: f 36 THR cc_start: 0.6725 (t) cc_final: 0.6443 (t) REVERT: m 93 ARG cc_start: 0.7574 (mtt180) cc_final: 0.6318 (mmt-90) REVERT: m 94 ARG cc_start: 0.8235 (mmt180) cc_final: 0.7586 (mmt180) REVERT: p 14 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7578 (tpp-160) REVERT: p 15 ASN cc_start: 0.8696 (p0) cc_final: 0.7912 (p0) REVERT: p 57 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8529 (mm110) outliers start: 107 outliers final: 78 residues processed: 516 average time/residue: 0.5781 time to fit residues: 481.5963 Evaluate side-chains 516 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 434 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 68 HIS Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 90 GLU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 128 SER Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 81 PHE Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 101 LEU Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 110 GLN Chi-restraints excluded: chain k residue 120 SER Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 7 GLN Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 57 CYS Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 79 PHE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 52 GLU Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 53 VAL Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 8 THR Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 75 LYS Chi-restraints excluded: chain p residue 79 ASP Chi-restraints excluded: chain p residue 94 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 313 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 279 optimal weight: 0.0980 chunk 155 optimal weight: 8.9990 chunk 320 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 337 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 66 GLN ** m 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 57293 Z= 0.238 Angle : 0.643 10.945 85230 Z= 0.324 Chirality : 0.036 0.296 10807 Planarity : 0.005 0.082 4930 Dihedral : 24.014 178.563 27744 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.86 % Favored : 91.89 % Rotamer: Outliers : 5.85 % Allowed : 17.86 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2366 helix: 0.46 (0.17), residues: 1015 sheet: -0.96 (0.27), residues: 354 loop : -1.88 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP k 53 HIS 0.037 0.001 HIS c 68 PHE 0.019 0.002 PHE n 16 TYR 0.023 0.002 TYR p 40 ARG 0.011 0.001 ARG e 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 468 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 PHE cc_start: 0.8559 (t80) cc_final: 0.8093 (t80) REVERT: c 28 TYR cc_start: 0.7869 (t80) cc_final: 0.7496 (t80) REVERT: c 113 GLN cc_start: 0.8399 (tp40) cc_final: 0.8175 (tp-100) REVERT: i 87 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5712 (pp) REVERT: l 39 THR cc_start: 0.8172 (m) cc_final: 0.7810 (p) REVERT: q 73 ARG cc_start: 0.6834 (mmm-85) cc_final: 0.6522 (ttp-170) REVERT: r 79 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6316 (t80) REVERT: s 66 MET cc_start: 0.7838 (mmp) cc_final: 0.7212 (mmp) REVERT: b 6 MET cc_start: 0.4217 (mtp) cc_final: 0.2837 (tpp) REVERT: b 168 LYS cc_start: 0.7233 (tptt) cc_final: 0.6675 (ttpp) REVERT: d 36 HIS cc_start: 0.7706 (m90) cc_final: 0.7495 (m90) REVERT: d 52 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: d 58 PHE cc_start: 0.7983 (m-80) cc_final: 0.7659 (m-10) REVERT: d 75 ASN cc_start: 0.8492 (t0) cc_final: 0.8156 (m-40) REVERT: d 98 TYR cc_start: 0.7375 (t80) cc_final: 0.7108 (t80) REVERT: d 193 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7030 (mp10) REVERT: f 8 VAL cc_start: 0.9024 (t) cc_final: 0.8678 (p) REVERT: f 43 TRP cc_start: 0.8183 (OUTLIER) cc_final: 0.7006 (p-90) REVERT: m 88 GLN cc_start: 0.8591 (mt0) cc_final: 0.8346 (mt0) REVERT: m 93 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6322 (mmt-90) REVERT: m 94 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7571 (mmt180) REVERT: p 14 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7628 (tpp-160) REVERT: p 15 ASN cc_start: 0.8724 (p0) cc_final: 0.8313 (p0) REVERT: p 57 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8514 (mm110) outliers start: 117 outliers final: 84 residues processed: 528 average time/residue: 0.5496 time to fit residues: 472.3598 Evaluate side-chains 543 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 454 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 99 VAL Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 182 ARG Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 128 SER Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 81 PHE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain k residue 95 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 120 SER Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 57 CYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 79 PHE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 52 GLU Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 42 ASN Chi-restraints excluded: chain m residue 53 VAL Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 8 THR Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 79 ASP Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 94 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 126 optimal weight: 8.9990 chunk 338 optimal weight: 0.0870 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 376 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 68 HIS ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN i 27 GLN i 86 HIS ** k 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.162 57293 Z= 0.367 Angle : 0.777 12.403 85230 Z= 0.386 Chirality : 0.041 0.323 10807 Planarity : 0.006 0.076 4930 Dihedral : 24.177 179.603 27744 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.27 % Favored : 89.52 % Rotamer: Outliers : 6.10 % Allowed : 18.96 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2366 helix: 0.27 (0.16), residues: 1012 sheet: -1.30 (0.26), residues: 365 loop : -1.99 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP s 34 HIS 0.009 0.002 HIS t 52 PHE 0.040 0.003 PHE c 129 TYR 0.033 0.003 TYR c 31 ARG 0.017 0.001 ARG c 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 471 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 PHE cc_start: 0.8635 (t80) cc_final: 0.8238 (t80) REVERT: c 28 TYR cc_start: 0.7826 (t80) cc_final: 0.7454 (t80) REVERT: c 195 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.7190 (mtm-85) REVERT: l 39 THR cc_start: 0.8439 (m) cc_final: 0.8137 (p) REVERT: o 77 ARG cc_start: 0.7353 (ttp-110) cc_final: 0.7136 (mtm110) REVERT: r 79 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7159 (t80) REVERT: n 16 PHE cc_start: 0.8530 (m-80) cc_final: 0.8176 (m-80) REVERT: b 6 MET cc_start: 0.4175 (mtp) cc_final: 0.3460 (tpp) REVERT: b 100 MET cc_start: 0.7362 (tpp) cc_final: 0.7132 (tpp) REVERT: b 168 LYS cc_start: 0.7362 (tptt) cc_final: 0.6815 (ttpp) REVERT: b 228 ARG cc_start: 0.2803 (ttt180) cc_final: 0.2328 (tpt170) REVERT: d 52 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: d 75 ASN cc_start: 0.8557 (t0) cc_final: 0.8054 (m-40) REVERT: d 98 TYR cc_start: 0.7360 (t80) cc_final: 0.7124 (t80) REVERT: d 136 ASP cc_start: 0.7574 (m-30) cc_final: 0.7121 (t0) REVERT: d 176 LEU cc_start: 0.6277 (mt) cc_final: 0.5889 (mp) REVERT: d 193 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7563 (mt0) REVERT: f 8 VAL cc_start: 0.9104 (t) cc_final: 0.8760 (p) REVERT: f 43 TRP cc_start: 0.8248 (OUTLIER) cc_final: 0.7163 (p-90) REVERT: m 54 THR cc_start: 0.8878 (p) cc_final: 0.8677 (p) REVERT: m 93 ARG cc_start: 0.7693 (mtt180) cc_final: 0.6406 (mmm-85) REVERT: m 94 ARG cc_start: 0.8193 (mmt180) cc_final: 0.7728 (mmt180) REVERT: p 15 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8475 (p0) REVERT: p 57 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8550 (mm110) outliers start: 122 outliers final: 88 residues processed: 531 average time/residue: 0.5508 time to fit residues: 476.7986 Evaluate side-chains 545 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 453 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 99 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 182 ARG Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 68 ASN Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 128 SER Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain i residue 131 ILE Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain k residue 95 VAL Chi-restraints excluded: chain k residue 110 GLN Chi-restraints excluded: chain k residue 120 SER Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain r residue 22 PHE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 57 CYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 79 PHE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 5 LYS Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 52 GLU Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 42 ASN Chi-restraints excluded: chain m residue 53 VAL Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 15 ASN Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 27 THR Chi-restraints excluded: chain p residue 79 ASP Chi-restraints excluded: chain p residue 94 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 362 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 214 optimal weight: 0.8980 chunk 274 optimal weight: 0.1980 chunk 212 optimal weight: 0.0770 chunk 316 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 374 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 228 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 68 HIS g 68 ASN h 121 GLN i 27 GLN ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 110 GLN ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 33 GLN r 56 ASN ** m 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 57293 Z= 0.144 Angle : 0.596 10.198 85230 Z= 0.302 Chirality : 0.034 0.331 10807 Planarity : 0.005 0.079 4930 Dihedral : 24.042 179.467 27744 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.10 % Favored : 92.69 % Rotamer: Outliers : 3.70 % Allowed : 21.91 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.17), residues: 2366 helix: 0.77 (0.17), residues: 1004 sheet: -0.93 (0.27), residues: 364 loop : -1.85 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP k 53 HIS 0.013 0.001 HIS n 8 PHE 0.014 0.001 PHE n 16 TYR 0.021 0.002 TYR r 32 ARG 0.009 0.000 ARG g 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 465 time to evaluate : 2.357 Fit side-chains revert: symmetry clash REVERT: c 10 PHE cc_start: 0.8512 (t80) cc_final: 0.8046 (t80) REVERT: c 28 TYR cc_start: 0.7788 (t80) cc_final: 0.7425 (t80) REVERT: c 55 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7319 (mt-10) REVERT: c 68 HIS cc_start: 0.7186 (OUTLIER) cc_final: 0.6104 (m90) REVERT: i 41 LEU cc_start: 0.7251 (mm) cc_final: 0.7045 (mm) REVERT: l 39 THR cc_start: 0.8045 (m) cc_final: 0.7701 (p) REVERT: o 43 LEU cc_start: 0.9125 (mm) cc_final: 0.8771 (mt) REVERT: q 82 LEU cc_start: 0.8777 (mp) cc_final: 0.8576 (mp) REVERT: q 90 LEU cc_start: 0.7584 (pt) cc_final: 0.7170 (pp) REVERT: r 79 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6310 (t80) REVERT: s 66 MET cc_start: 0.7427 (mmp) cc_final: 0.7075 (mmp) REVERT: n 8 HIS cc_start: 0.8706 (t70) cc_final: 0.8500 (t-90) REVERT: b 6 MET cc_start: 0.4142 (mtp) cc_final: 0.3664 (tpp) REVERT: b 21 ARG cc_start: 0.6632 (mtt90) cc_final: 0.6422 (mmt90) REVERT: b 168 LYS cc_start: 0.7228 (tptt) cc_final: 0.6669 (ttpp) REVERT: d 52 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7400 (tt0) REVERT: d 75 ASN cc_start: 0.8460 (t0) cc_final: 0.8047 (m-40) REVERT: d 98 TYR cc_start: 0.7258 (t80) cc_final: 0.6982 (t80) REVERT: d 136 ASP cc_start: 0.7256 (m-30) cc_final: 0.6778 (t0) REVERT: f 8 VAL cc_start: 0.9067 (t) cc_final: 0.8650 (p) REVERT: f 43 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.7001 (p-90) REVERT: m 22 ILE cc_start: 0.8286 (mt) cc_final: 0.8084 (mm) REVERT: m 93 ARG cc_start: 0.7462 (mtt180) cc_final: 0.6291 (mmt-90) REVERT: m 94 ARG cc_start: 0.8094 (mmt180) cc_final: 0.7523 (mmt180) REVERT: p 15 ASN cc_start: 0.8755 (p0) cc_final: 0.8398 (p0) REVERT: p 57 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8565 (mm110) outliers start: 74 outliers final: 55 residues processed: 504 average time/residue: 0.6088 time to fit residues: 502.2208 Evaluate side-chains 500 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 442 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 68 HIS Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 99 VAL Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain k residue 120 SER Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain r residue 57 CYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 79 PHE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 42 ASN Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 79 ASP Chi-restraints excluded: chain p residue 86 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 231 optimal weight: 0.0070 chunk 149 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 255 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 68 HIS i 27 GLN i 66 GLN k 27 HIS ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 84 GLN ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 33 GLN s 52 HIS s 69 HIS ** m 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 57293 Z= 0.267 Angle : 0.669 11.212 85230 Z= 0.334 Chirality : 0.037 0.489 10807 Planarity : 0.005 0.077 4930 Dihedral : 24.000 179.790 27744 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.81 % Favored : 89.94 % Rotamer: Outliers : 4.55 % Allowed : 21.66 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2366 helix: 0.74 (0.17), residues: 998 sheet: -1.09 (0.27), residues: 366 loop : -1.83 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP k 53 HIS 0.015 0.001 HIS c 68 PHE 0.016 0.002 PHE s 80 TYR 0.022 0.002 TYR r 32 ARG 0.007 0.001 ARG i 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 453 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 10 PHE cc_start: 0.8534 (t80) cc_final: 0.8108 (t80) REVERT: c 28 TYR cc_start: 0.7865 (t80) cc_final: 0.7514 (t80) REVERT: c 68 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6870 (m-70) REVERT: c 195 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.7194 (mtm-85) REVERT: i 111 GLN cc_start: 0.8200 (tp40) cc_final: 0.7977 (tt0) REVERT: k 84 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: l 39 THR cc_start: 0.8196 (m) cc_final: 0.7875 (p) REVERT: q 82 LEU cc_start: 0.8938 (mp) cc_final: 0.8626 (mp) REVERT: q 92 GLU cc_start: 0.7258 (mp0) cc_final: 0.7042 (mp0) REVERT: r 79 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7056 (t80) REVERT: n 16 PHE cc_start: 0.8530 (m-80) cc_final: 0.7776 (m-80) REVERT: b 6 MET cc_start: 0.4165 (mtp) cc_final: 0.3681 (tpp) REVERT: b 168 LYS cc_start: 0.7311 (tptt) cc_final: 0.6779 (ttpp) REVERT: d 52 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: d 75 ASN cc_start: 0.8447 (t0) cc_final: 0.7966 (m-40) REVERT: d 98 TYR cc_start: 0.7317 (t80) cc_final: 0.7022 (t80) REVERT: d 108 MET cc_start: 0.7136 (tpp) cc_final: 0.6935 (tmm) REVERT: d 136 ASP cc_start: 0.7505 (m-30) cc_final: 0.7014 (t0) REVERT: d 193 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7345 (tp-100) REVERT: f 8 VAL cc_start: 0.9091 (t) cc_final: 0.8688 (p) REVERT: f 43 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7093 (p-90) REVERT: m 81 LYS cc_start: 0.7632 (ptmt) cc_final: 0.7379 (mtmm) REVERT: m 93 ARG cc_start: 0.7601 (mtt180) cc_final: 0.6420 (mmt-90) REVERT: m 94 ARG cc_start: 0.8100 (mmt180) cc_final: 0.7522 (mmt180) REVERT: m 104 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8410 (ttmm) REVERT: p 15 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8463 (p0) REVERT: p 57 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8540 (mm110) outliers start: 91 outliers final: 77 residues processed: 502 average time/residue: 0.5855 time to fit residues: 481.0859 Evaluate side-chains 525 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 441 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 68 HIS Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 99 VAL Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 182 ARG Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 63 GLN Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 79 ASP Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain k residue 84 GLN Chi-restraints excluded: chain k residue 95 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 120 SER Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain o residue 7 GLN Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain q residue 33 GLN Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain r residue 22 PHE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 57 CYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 79 PHE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 52 GLU Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 42 ASN Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 104 LYS Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 15 ASN Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 75 LYS Chi-restraints excluded: chain p residue 79 ASP Chi-restraints excluded: chain p residue 86 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 341 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 349 optimal weight: 3.9990 chunk 210 optimal weight: 0.2980 chunk 152 optimal weight: 0.8980 chunk 274 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 348 optimal weight: 8.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 143 GLN g 68 ASN i 27 GLN ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 84 GLN ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 57293 Z= 0.162 Angle : 0.600 10.503 85230 Z= 0.303 Chirality : 0.034 0.552 10807 Planarity : 0.005 0.077 4930 Dihedral : 23.974 179.480 27744 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.82 % Favored : 91.97 % Rotamer: Outliers : 3.85 % Allowed : 22.26 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.84 (0.17), residues: 2366 helix: 0.83 (0.17), residues: 1004 sheet: -0.96 (0.27), residues: 365 loop : -1.85 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP k 53 HIS 0.016 0.001 HIS c 68 PHE 0.011 0.001 PHE s 80 TYR 0.021 0.002 TYR d 130 ARG 0.008 0.000 ARG i 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 447 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 10 PHE cc_start: 0.8512 (t80) cc_final: 0.8051 (t80) REVERT: c 28 TYR cc_start: 0.7804 (t80) cc_final: 0.7445 (t80) REVERT: c 51 ILE cc_start: 0.8237 (pt) cc_final: 0.7943 (pt) REVERT: i 147 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8645 (p90) REVERT: l 39 THR cc_start: 0.8060 (m) cc_final: 0.7721 (p) REVERT: q 82 LEU cc_start: 0.8861 (mp) cc_final: 0.8650 (mp) REVERT: r 79 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6824 (t80) REVERT: n 16 PHE cc_start: 0.8543 (m-80) cc_final: 0.7844 (m-10) REVERT: b 6 MET cc_start: 0.4063 (mtp) cc_final: 0.3782 (tpp) REVERT: b 168 LYS cc_start: 0.7274 (tptt) cc_final: 0.6720 (ttpp) REVERT: d 52 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: d 75 ASN cc_start: 0.8461 (t0) cc_final: 0.8043 (m-40) REVERT: d 98 TYR cc_start: 0.7258 (t80) cc_final: 0.7043 (t80) REVERT: d 136 ASP cc_start: 0.7288 (m-30) cc_final: 0.6836 (t0) REVERT: f 8 VAL cc_start: 0.9057 (t) cc_final: 0.8640 (p) REVERT: f 43 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.6998 (p-90) REVERT: m 22 ILE cc_start: 0.8088 (mt) cc_final: 0.7884 (mm) REVERT: m 81 LYS cc_start: 0.7543 (ptmt) cc_final: 0.7310 (mtmm) REVERT: m 93 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6292 (mmt-90) REVERT: m 94 ARG cc_start: 0.8065 (mmt180) cc_final: 0.7503 (mmt180) REVERT: p 15 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8441 (p0) REVERT: p 57 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8512 (mm110) outliers start: 77 outliers final: 64 residues processed: 491 average time/residue: 0.5392 time to fit residues: 434.9136 Evaluate side-chains 509 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 440 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 99 VAL Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 162 VAL Chi-restraints excluded: chain e residue 182 ARG Chi-restraints excluded: chain h residue 58 LYS Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain i residue 147 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 120 SER Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain o residue 7 GLN Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 57 CYS Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 79 PHE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 42 ASN Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 15 ASN Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 75 LYS Chi-restraints excluded: chain p residue 79 ASP Chi-restraints excluded: chain p residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 229 optimal weight: 0.8980 chunk 369 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 387 optimal weight: 2.9990 chunk 356 optimal weight: 0.5980 chunk 308 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 238 optimal weight: 0.3980 chunk 189 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN i 27 GLN i 61 ASN ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 57293 Z= 0.141 Angle : 0.565 10.522 85230 Z= 0.284 Chirality : 0.032 0.450 10807 Planarity : 0.005 0.077 4930 Dihedral : 23.854 179.970 27744 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.45 % Favored : 91.38 % Rotamer: Outliers : 3.25 % Allowed : 23.06 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2366 helix: 1.08 (0.17), residues: 1005 sheet: -0.76 (0.27), residues: 371 loop : -1.78 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP k 53 HIS 0.010 0.001 HIS c 68 PHE 0.017 0.001 PHE b 30 TYR 0.020 0.001 TYR r 32 ARG 0.009 0.000 ARG c 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 450 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 10 PHE cc_start: 0.8538 (t80) cc_final: 0.8069 (t80) REVERT: c 28 TYR cc_start: 0.7741 (t80) cc_final: 0.7437 (t80) REVERT: l 39 THR cc_start: 0.8052 (m) cc_final: 0.7723 (p) REVERT: r 52 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7743 (tpp80) REVERT: r 79 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6342 (t80) REVERT: t 83 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6603 (tp) REVERT: n 16 PHE cc_start: 0.8601 (m-80) cc_final: 0.8041 (m-10) REVERT: b 6 MET cc_start: 0.3831 (mtp) cc_final: 0.3478 (tpp) REVERT: b 168 LYS cc_start: 0.7224 (tptt) cc_final: 0.6695 (ttpp) REVERT: b 184 ILE cc_start: 0.7710 (mt) cc_final: 0.7498 (mp) REVERT: b 228 ARG cc_start: 0.2796 (ttt180) cc_final: 0.2329 (tpt170) REVERT: d 52 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7528 (tt0) REVERT: d 75 ASN cc_start: 0.8383 (t0) cc_final: 0.8041 (m-40) REVERT: d 98 TYR cc_start: 0.7330 (t80) cc_final: 0.7109 (t80) REVERT: d 108 MET cc_start: 0.7063 (tpp) cc_final: 0.6604 (tmm) REVERT: f 8 VAL cc_start: 0.8963 (t) cc_final: 0.8547 (p) REVERT: m 93 ARG cc_start: 0.7322 (mtt180) cc_final: 0.6255 (mmt-90) REVERT: p 15 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8133 (p0) REVERT: p 57 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8413 (mm110) outliers start: 65 outliers final: 55 residues processed: 485 average time/residue: 0.5481 time to fit residues: 435.5442 Evaluate side-chains 490 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 432 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 165 SER Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 99 VAL Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 162 VAL Chi-restraints excluded: chain e residue 182 ARG Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 90 ILE Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain k residue 120 SER Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 57 CYS Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 79 PHE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 129 SER Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 15 ASN Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 75 LYS Chi-restraints excluded: chain p residue 79 ASP Chi-restraints excluded: chain p residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 245 optimal weight: 0.9990 chunk 328 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 309 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 317 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 99 GLN c 107 ASN c 143 GLN i 27 GLN i 61 ASN i 111 GLN k 27 HIS ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133070 restraints weight = 85125.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133542 restraints weight = 79330.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.134141 restraints weight = 54674.342| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 57293 Z= 0.349 Angle : 0.752 12.835 85230 Z= 0.371 Chirality : 0.040 0.447 10807 Planarity : 0.006 0.076 4930 Dihedral : 23.967 179.950 27744 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.14 % Favored : 89.60 % Rotamer: Outliers : 3.85 % Allowed : 22.81 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.04 (0.17), residues: 2366 helix: 0.67 (0.16), residues: 1003 sheet: -1.15 (0.27), residues: 361 loop : -1.92 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP k 53 HIS 0.013 0.002 HIS t 52 PHE 0.035 0.002 PHE s 80 TYR 0.024 0.003 TYR o 78 ARG 0.011 0.001 ARG i 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8429.39 seconds wall clock time: 151 minutes 10.87 seconds (9070.87 seconds total)