Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:59:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2023/5zeu_6923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2023/5zeu_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_2023/5zeu_6923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2023/5zeu_6923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2023/5zeu_6923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeu_6923/02_2023/5zeu_6923.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 21.59, per 1000 atoms: 0.41 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 2.5 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: 16.19 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: 34.29 Time building geometry restraints manager: 21.97 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: 29535 35.62 - 71.23: 1274 71.23 - 106.85: 108 106.85 - 142.46: 18 142.46 - 178.08: 21 Dihedral angle restraints: 30956 sinusoidal: 24077 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 30953 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 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. 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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.980 Check model and map are aligned: 0.580 Process input model: 130.000 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.360 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 16.392 178.080 26525 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 % 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 *********************** 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 : 2.432 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 outliers start: 28 outliers final: 11 residues processed: 689 average time/residue: 0.6442 time to fit residues: 680.8402 Evaluate side-chains 499 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 488 time to evaluate : 2.458 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.7007 time to fit residues: 14.2725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 328 optimal weight: 4.9990 chunk 294 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 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: 6.9990 overall best weight: 1.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 86 HIS j 99 ASN k 31 HIS k 78 ASN l 6 GLN l 29 GLN ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS ** q 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 ASN 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 m 88 GLN p 15 ASN p 57 GLN p 107 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.151 57293 Z= 0.269 Angle : 0.773 10.621 85230 Z= 0.391 Chirality : 0.042 0.272 10807 Planarity : 0.006 0.076 4930 Dihedral : 16.095 179.112 21695 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.41 % Favored : 91.12 % Rotamer Outliers : 4.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.31 % 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: -2.54 (0.16), residues: 2366 helix: -1.06 (0.15), residues: 1018 sheet: -1.47 (0.25), residues: 374 loop : -2.37 (0.17), residues: 974 *********************** 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 617 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 521 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 59 residues processed: 560 average time/residue: 0.5834 time to fit residues: 526.3549 Evaluate side-chains 520 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 461 time to evaluate : 2.419 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.4033 time to fit residues: 48.2922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 196 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 294 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 353 optimal weight: 0.0050 chunk 382 optimal weight: 0.9980 chunk 315 optimal weight: 0.8980 chunk 350 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 283 optimal weight: 0.7980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 97 GLN c 101 ASN g 68 ASN h 63 GLN h 121 GLN i 61 ASN ** i 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 66 GLN ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 ASN j 64 HIS ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 7 GLN o 14 GLN q 62 HIS r 56 ASN m 101 GLN p 57 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 57293 Z= 0.155 Angle : 0.600 10.416 85230 Z= 0.307 Chirality : 0.035 0.282 10807 Planarity : 0.005 0.077 4930 Dihedral : 15.476 178.694 21695 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.40 % Favored : 92.31 % Rotamer Outliers : 2.65 % 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: -1.60 (0.16), residues: 2366 helix: -0.05 (0.16), residues: 1020 sheet: -1.13 (0.26), residues: 362 loop : -2.09 (0.18), residues: 984 *********************** 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 542 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 489 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 27 residues processed: 515 average time/residue: 0.5520 time to fit residues: 463.6882 Evaluate side-chains 461 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 434 time to evaluate : 2.408 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3680 time to fit residues: 21.7388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 349 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 39 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 355 optimal weight: 7.9990 chunk 376 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 h 63 GLN h 117 GLN i 61 ASN j 56 HIS ** k 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 7 GLN o 14 GLN t 74 ASN m 63 ASN p 57 GLN u 17 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.169 57293 Z= 0.326 Angle : 0.756 9.847 85230 Z= 0.378 Chirality : 0.040 0.300 10807 Planarity : 0.006 0.073 4930 Dihedral : 15.696 179.459 21695 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.59 % Favored : 90.07 % Rotamer Outliers : 4.45 % 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: -1.47 (0.17), residues: 2366 helix: 0.09 (0.16), residues: 1005 sheet: -1.27 (0.26), residues: 367 loop : -1.94 (0.19), residues: 994 *********************** 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 574 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 485 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 55 residues processed: 527 average time/residue: 0.5806 time to fit residues: 491.2620 Evaluate side-chains 503 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 448 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.3843 time to fit residues: 42.6991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 5 optimal weight: 6.9990 chunk 279 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 320 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 192 optimal weight: 0.0980 chunk 337 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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** ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN i 61 ASN 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 65 ASN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 57 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.106 57293 Z= 0.206 Angle : 0.623 9.394 85230 Z= 0.316 Chirality : 0.036 0.313 10807 Planarity : 0.005 0.080 4930 Dihedral : 15.362 178.560 21695 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.57 % Favored : 92.18 % Rotamer Outliers : 2.45 % 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: -1.15 (0.17), residues: 2366 helix: 0.41 (0.16), residues: 1014 sheet: -0.99 (0.26), residues: 362 loop : -1.89 (0.19), residues: 990 *********************** 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 508 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 459 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 23 residues processed: 487 average time/residue: 0.5892 time to fit residues: 465.2584 Evaluate side-chains 454 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 431 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4597 time to fit residues: 22.0198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 126 optimal weight: 10.0000 chunk 338 optimal weight: 0.0870 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 376 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 chunk 174 optimal weight: 0.0770 chunk 31 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 overall best weight: 3.0322 ------------------------------------------------------------------------------- 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 61 ASN ** i 146 GLN ** 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** o 7 GLN q 33 GLN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.151 57293 Z= 0.329 Angle : 0.736 10.691 85230 Z= 0.368 Chirality : 0.040 0.306 10807 Planarity : 0.006 0.077 4930 Dihedral : 15.603 179.790 21695 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.97 % Favored : 89.81 % Rotamer Outliers : 3.10 % 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: -1.25 (0.17), residues: 2366 helix: 0.35 (0.16), residues: 1008 sheet: -1.25 (0.26), residues: 367 loop : -1.88 (0.19), residues: 991 *********************** 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 520 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 458 time to evaluate : 2.515 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 44 residues processed: 479 average time/residue: 0.5729 time to fit residues: 444.2117 Evaluate side-chains 482 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 438 time to evaluate : 2.437 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3779 time to fit residues: 34.5797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 362 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 214 optimal weight: 0.3980 chunk 274 optimal weight: 3.9990 chunk 212 optimal weight: 0.0470 chunk 316 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 374 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 3 GLN ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 27 GLN i 61 ASN ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 66 GLN ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 57293 Z= 0.167 Angle : 0.597 9.839 85230 Z= 0.303 Chirality : 0.034 0.310 10807 Planarity : 0.005 0.079 4930 Dihedral : 15.257 178.656 21695 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.48 % Favored : 92.31 % Rotamer Outliers : 1.20 % 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: -0.94 (0.17), residues: 2366 helix: 0.65 (0.17), residues: 1005 sheet: -1.08 (0.26), residues: 365 loop : -1.76 (0.19), residues: 996 *********************** 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 475 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 451 time to evaluate : 2.457 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 463 average time/residue: 0.5691 time to fit residues: 429.8009 Evaluate side-chains 448 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 431 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4187 time to fit residues: 15.7757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 231 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 255 optimal weight: 0.0980 chunk 185 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 113 GLN h 63 GLN i 27 GLN i 61 ASN k 31 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** o 7 GLN q 33 GLN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 66 GLN m 63 ASN p 57 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 57293 Z= 0.252 Angle : 0.656 9.707 85230 Z= 0.330 Chirality : 0.036 0.287 10807 Planarity : 0.005 0.079 4930 Dihedral : 15.323 179.759 21695 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.59 % Favored : 90.19 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.05 (0.17), residues: 2366 helix: 0.54 (0.16), residues: 1015 sheet: -1.14 (0.26), residues: 366 loop : -1.82 (0.19), residues: 985 *********************** 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 497 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 455 time to evaluate : 2.418 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 28 residues processed: 471 average time/residue: 0.5625 time to fit residues: 431.4123 Evaluate side-chains 460 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 432 time to evaluate : 2.419 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3829 time to fit residues: 23.1149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 341 optimal weight: 2.9990 chunk 359 optimal weight: 0.8980 chunk 327 optimal weight: 0.7980 chunk 349 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 274 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 315 optimal weight: 4.9990 chunk 330 optimal weight: 0.7980 chunk 348 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 27 GLN i 61 ASN 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** s 52 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 57293 Z= 0.148 Angle : 0.578 9.783 85230 Z= 0.294 Chirality : 0.033 0.298 10807 Planarity : 0.005 0.081 4930 Dihedral : 15.119 179.205 21695 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.57 % Favored : 92.22 % Rotamer Outliers : 0.60 % 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: -0.82 (0.17), residues: 2366 helix: 0.75 (0.17), residues: 1008 sheet: -0.98 (0.27), residues: 369 loop : -1.72 (0.20), residues: 989 *********************** 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 459 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 447 time to evaluate : 2.446 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 452 average time/residue: 0.5741 time to fit residues: 422.7668 Evaluate side-chains 441 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 431 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4347 time to fit residues: 10.6046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 225 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 387 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 63 GLN 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** o 7 GLN t 3 ASN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 57293 Z= 0.232 Angle : 0.631 11.160 85230 Z= 0.317 Chirality : 0.035 0.293 10807 Planarity : 0.005 0.081 4930 Dihedral : 15.155 179.631 21695 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.38 % Favored : 90.41 % Rotamer Outliers : 0.65 % 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: -0.91 (0.17), residues: 2366 helix: 0.65 (0.16), residues: 1007 sheet: -0.93 (0.27), residues: 365 loop : -1.78 (0.19), residues: 994 ********************** 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 456 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 443 time to evaluate : 2.494 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 448 average time/residue: 0.5709 time to fit residues: 416.2066 Evaluate side-chains 447 residues out of total 1999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 438 time to evaluate : 2.480 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4021 time to fit residues: 9.5838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 245 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 309 optimal weight: 0.5980 chunk 129 optimal weight: 8.9990 chunk 317 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 52 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.151732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131555 restraints weight = 85715.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132860 restraints weight = 69395.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133004 restraints weight = 45722.422| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.108 57293 Z= 0.383 Angle : 0.788 10.720 85230 Z= 0.390 Chirality : 0.042 0.326 10807 Planarity : 0.006 0.081 4930 Dihedral : 15.700 178.300 21695 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.61 % Favored : 89.14 % Rotamer Outliers : 1.05 % 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: -1.34 (0.17), residues: 2366 helix: 0.27 (0.16), residues: 1004 sheet: -1.20 (0.26), residues: 366 loop : -1.95 (0.19), residues: 996 =============================================================================== Job complete usr+sys time: 8011.37 seconds wall clock time: 144 minutes 18.08 seconds (8658.08 seconds total)