Starting phenix.real_space_refine (version: dev) on Sat Dec 17 01:54:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/12_2022/5v7q_8641_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/12_2022/5v7q_8641.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/5v7q_8641/12_2022/5v7q_8641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/12_2022/5v7q_8641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/12_2022/5v7q_8641_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/12_2022/5v7q_8641_updated.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= 0.012 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "Q ASP 97": "OD1" <-> "OD2" Residue "R TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 94306 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 421 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 358 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 345 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "A" Number of atoms: 66956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66956 Classifications: {'RNA': 3118} Modifications used: {'rna2p_pur': 299, 'rna2p_pyr': 163, 'rna3p_pur': 1484, 'rna3p_pyr': 1172} Link IDs: {'rna2p': 462, 'rna3p': 2655} Chain breaks: 1 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 11, 'rna3p': 103} Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 9, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1335 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1060 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 886 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 742 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 759 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "X" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 476 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Y" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 541 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'917': 1} Classifications: {'undetermined': 1} Time building chain proxies: 40.20, per 1000 atoms: 0.43 Number of scatterers: 94306 At special positions: 0 Unit cell: (213.815, 225.295, 233.905, 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 53 16.00 P 3233 15.00 O 26869 8.00 N 17745 7.00 C 46406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.42 Conformation dependent library (CDL) restraints added in 3.5 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 42 sheets defined 22.7% alpha, 14.7% beta 795 base pairs and 1585 stacking pairs defined. Time for finding SS restraints: 38.71 Creating SS restraints... Processing helix chain '0' and resid 10 through 18 removed outlier: 4.218A pdb=" N SER 0 15 " --> pdb=" O SER 0 11 " (cutoff:3.500A) Processing helix chain '0' and resid 41 through 49 removed outlier: 4.866A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) Processing helix chain '2' and resid 12 through 19 Processing helix chain '2' and resid 21 through 26 removed outlier: 3.838A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 40 removed outlier: 3.551A pdb=" N SER 2 32 " --> pdb=" O ARG 2 28 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 11 No H-bonds generated for 'chain '3' and resid 8 through 11' Processing helix chain '3' and resid 38 through 44 Processing helix chain '3' and resid 55 through 62 removed outlier: 4.343A pdb=" N SER 3 60 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) Processing helix chain '6' and resid 39 through 41 No H-bonds generated for 'chain '6' and resid 39 through 41' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'D' and resid 42 through 45 No H-bonds generated for 'chain 'D' and resid 42 through 45' Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 126 through 129 No H-bonds generated for 'chain 'D' and resid 126 through 129' Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 37 through 51 Processing helix chain 'E' and resid 110 through 126 Processing helix chain 'E' and resid 144 through 154 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 192 through 196 Processing helix chain 'E' and resid 204 through 213 Processing helix chain 'F' and resid 13 through 26 Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 55 through 67 removed outlier: 4.312A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 108 Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'G' and resid 4 through 6 No H-bonds generated for 'chain 'G' and resid 4 through 6' Processing helix chain 'G' and resid 61 through 81 Processing helix chain 'G' and resid 139 through 148 removed outlier: 3.623A pdb=" N ILE G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 46 Processing helix chain 'J' and resid 25 through 37 Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 66 through 69 No H-bonds generated for 'chain 'J' and resid 66 through 69' Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 97 through 108 Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.728A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 117 No H-bonds generated for 'chain 'K' and resid 114 through 117' Processing helix chain 'L' and resid 5 through 7 No H-bonds generated for 'chain 'L' and resid 5 through 7' Processing helix chain 'L' and resid 39 through 42 No H-bonds generated for 'chain 'L' and resid 39 through 42' Processing helix chain 'L' and resid 56 through 59 No H-bonds generated for 'chain 'L' and resid 56 through 59' Processing helix chain 'L' and resid 79 through 85 Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'M' and resid 44 through 57 Processing helix chain 'M' and resid 111 through 124 Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 57 Proline residue: N 46 - end of helix removed outlier: 3.619A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 67 Processing helix chain 'N' and resid 74 through 81 Processing helix chain 'N' and resid 83 through 89 removed outlier: 4.868A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 22 removed outlier: 3.671A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 72 through 90 removed outlier: 3.964A pdb=" N VAL O 77 " --> pdb=" O LYS O 73 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 117 Processing helix chain 'P' and resid 2 through 11 Proline residue: P 10 - end of helix Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'Q' and resid 7 through 21 removed outlier: 3.883A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 71 removed outlier: 3.857A pdb=" N GLU Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 86 Processing helix chain 'Q' and resid 92 through 101 removed outlier: 3.687A pdb=" N ILE Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'S' and resid 24 through 34 removed outlier: 4.101A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 47 Processing helix chain 'S' and resid 55 through 70 Processing helix chain 'S' and resid 99 through 101 No H-bonds generated for 'chain 'S' and resid 99 through 101' Processing helix chain 'T' and resid 18 through 22 Processing helix chain 'T' and resid 25 through 27 No H-bonds generated for 'chain 'T' and resid 25 through 27' Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 68 through 70 No H-bonds generated for 'chain 'U' and resid 68 through 70' Processing helix chain 'V' and resid 19 through 27 Processing helix chain 'V' and resid 53 through 56 No H-bonds generated for 'chain 'V' and resid 53 through 56' Processing helix chain 'X' and resid 53 through 57 Processing helix chain 'Y' and resid 7 through 11 Processing helix chain 'Y' and resid 16 through 38 Processing helix chain 'Y' and resid 46 through 65 Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 43 through 49 Processing sheet with id= A, first strand: chain '1' and resid 37 through 42 Processing sheet with id= B, first strand: chain '1' and resid 11 through 14 removed outlier: 3.687A pdb=" N TYR 1 23 " --> pdb=" O LEU 1 13 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '3' and resid 14 through 16 removed outlier: 3.727A pdb=" N ARG 3 15 " --> pdb=" O VAL 3 23 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL 3 23 " --> pdb=" O ARG 3 15 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '4' and resid 15 through 19 Processing sheet with id= E, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= F, first strand: chain 'C' and resid 101 through 106 removed outlier: 3.864A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS C 96 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL C 79 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= H, first strand: chain 'C' and resid 172 through 176 Processing sheet with id= I, first strand: chain 'D' and resid 5 through 9 removed outlier: 6.085A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 13 through 17 removed outlier: 5.808A pdb=" N LYS D 195 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL D 182 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= L, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.500A pdb=" N GLY D 122 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 170 " --> pdb=" O GLY D 122 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 130 through 132 removed outlier: 6.632A pdb=" N VAL E 200 " --> pdb=" O HIS E 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 160 through 163 Processing sheet with id= O, first strand: chain 'F' and resid 94 through 98 removed outlier: 7.326A pdb=" N VAL F 164 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL F 41 " --> pdb=" O ASN F 162 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN F 162 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL F 43 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP F 160 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 23 through 26 Processing sheet with id= Q, first strand: chain 'G' and resid 42 through 45 Processing sheet with id= R, first strand: chain 'G' and resid 84 through 89 removed outlier: 6.330A pdb=" N THR G 133 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL G 126 " --> pdb=" O THR G 133 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER G 135 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE G 124 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 3 through 5 Processing sheet with id= T, first strand: chain 'J' and resid 137 through 139 removed outlier: 6.803A pdb=" N TRP J 15 " --> pdb=" O VAL J 138 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE J 18 " --> pdb=" O PHE J 53 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE J 55 " --> pdb=" O ILE J 18 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= V, first strand: chain 'K' and resid 7 through 9 removed outlier: 6.742A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 75 through 78 Processing sheet with id= X, first strand: chain 'M' and resid 40 through 43 removed outlier: 3.994A pdb=" N TRP M 92 " --> pdb=" O LEU M 74 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.583A pdb=" N MET N 110 " --> pdb=" O ILE N 100 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 32 through 37 removed outlier: 4.437A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 82 through 87 removed outlier: 3.965A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N LYS P 43 " --> pdb=" O GLU P 63 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU P 63 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG P 49 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR P 57 " --> pdb=" O ARG P 49 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'R' and resid 13 through 17 removed outlier: 3.627A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS R 9 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL R 40 " --> pdb=" O LYS R 9 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 21 through 26 removed outlier: 3.957A pdb=" N GLY R 63 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 74 through 79 Processing sheet with id= AE, first strand: chain 'S' and resid 13 through 17 removed outlier: 3.734A pdb=" N THR S 83 " --> pdb=" O VAL S 116 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU S 118 " --> pdb=" O VAL S 81 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL S 81 " --> pdb=" O GLU S 118 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'S' and resid 92 through 97 removed outlier: 3.683A pdb=" N ALA S 92 " --> pdb=" O ARG S 108 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.679A pdb=" N LEU T 32 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR T 30 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER T 56 " --> pdb=" O THR T 85 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'U' and resid 20 through 22 Processing sheet with id= AI, first strand: chain 'U' and resid 65 through 67 removed outlier: 3.794A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 7 through 10 Processing sheet with id= AK, first strand: chain 'V' and resid 41 through 45 removed outlier: 3.725A pdb=" N ILE V 31 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'V' and resid 105 through 109 Processing sheet with id= AM, first strand: chain 'V' and resid 121 through 124 Processing sheet with id= AN, first strand: chain 'X' and resid 13 through 16 Processing sheet with id= AO, first strand: chain 'X' and resid 33 through 36 Processing sheet with id= AP, first strand: chain 'Z' and resid 35 through 37 670 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2062 hydrogen bonds 3530 hydrogen bond angles 0 basepair planarities 795 basepair parallelities 1585 stacking parallelities Total time for adding SS restraints: 150.57 Time building geometry restraints manager: 43.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8727 1.31 - 1.43: 46959 1.43 - 1.56: 40745 1.56 - 1.69: 6464 1.69 - 1.81: 88 Bond restraints: 102983 Sorted by residual: bond pdb=" C02 917 A5001 " pdb=" N04 917 A5001 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C09 917 A5001 " pdb=" O11 917 A5001 " ideal model delta sigma weight residual 1.336 1.439 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C09 917 A5001 " pdb=" N08 917 A5001 " ideal model delta sigma weight residual 1.366 1.453 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C15 917 A5001 " pdb=" C18 917 A5001 " ideal model delta sigma weight residual 1.459 1.385 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CB PHE 2 21 " pdb=" CG PHE 2 21 " ideal model delta sigma weight residual 1.502 1.439 0.063 2.30e-02 1.89e+03 7.45e+00 ... (remaining 102978 not shown) Histogram of bond angle deviations from ideal: 94.99 - 103.18: 7839 103.18 - 111.38: 56973 111.38 - 119.57: 45083 119.57 - 127.76: 39040 127.76 - 135.96: 6297 Bond angle restraints: 155232 Sorted by residual: angle pdb=" N LYS K 113 " pdb=" CA LYS K 113 " pdb=" C LYS K 113 " ideal model delta sigma weight residual 114.62 109.18 5.44 1.14e+00 7.69e-01 2.28e+01 angle pdb=" O4' A A1272 " pdb=" C1' A A1272 " pdb=" N9 A A1272 " ideal model delta sigma weight residual 108.20 114.68 -6.48 1.50e+00 4.44e-01 1.87e+01 angle pdb=" N ARG N 9 " pdb=" CA ARG N 9 " pdb=" C ARG N 9 " ideal model delta sigma weight residual 110.53 105.01 5.52 1.29e+00 6.01e-01 1.83e+01 angle pdb=" O4' U A 719 " pdb=" C1' U A 719 " pdb=" N1 U A 719 " ideal model delta sigma weight residual 108.20 114.33 -6.13 1.50e+00 4.44e-01 1.67e+01 angle pdb=" C PHE R 79 " pdb=" N LYS R 80 " pdb=" CA LYS R 80 " ideal model delta sigma weight residual 121.71 116.30 5.41 1.39e+00 5.18e-01 1.52e+01 ... (remaining 155227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 53437 35.96 - 71.92: 860 71.92 - 107.88: 62 107.88 - 143.85: 4 143.85 - 179.81: 12 Dihedral angle restraints: 54375 sinusoidal: 45317 harmonic: 9058 Sorted by residual: dihedral pdb=" O4' C A2309 " pdb=" C1' C A2309 " pdb=" N1 C A2309 " pdb=" C2 C A2309 " ideal model delta sinusoidal sigma weight residual -160.00 11.07 -171.07 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C A 946 " pdb=" C1' C A 946 " pdb=" N1 C A 946 " pdb=" C2 C A 946 " ideal model delta sinusoidal sigma weight residual -160.00 10.10 -170.10 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C A1517 " pdb=" C1' C A1517 " pdb=" N1 C A1517 " pdb=" C2 C A1517 " ideal model delta sinusoidal sigma weight residual 200.00 31.67 168.33 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 54372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 17876 0.071 - 0.143: 1910 0.143 - 0.214: 164 0.214 - 0.285: 15 0.285 - 0.357: 4 Chirality restraints: 19969 Sorted by residual: chirality pdb=" C1' U A2386 " pdb=" O4' U A2386 " pdb=" C2' U A2386 " pdb=" N1 U A2386 " both_signs ideal model delta sigma weight residual False 2.47 2.11 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C1' G A 880 " pdb=" O4' G A 880 " pdb=" C2' G A 880 " pdb=" N9 G A 880 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C3' U A1567 " pdb=" C4' U A1567 " pdb=" O3' U A1567 " pdb=" C2' U A1567 " both_signs ideal model delta sigma weight residual False -2.48 -2.18 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 19966 not shown) Planarity restraints: 7675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 107 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO C 108 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 108 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 108 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 69 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO M 70 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO M 70 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO M 70 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 31 " -0.060 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO H 32 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " -0.050 5.00e-02 4.00e+02 ... (remaining 7672 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 1779 2.60 - 3.17: 75777 3.17 - 3.75: 182051 3.75 - 4.32: 243328 4.32 - 4.90: 331939 Nonbonded interactions: 834874 Sorted by model distance: nonbonded pdb=" O2' G A2746 " pdb=" O2' U A2792 " model vdw 2.022 2.440 nonbonded pdb=" O2' G A 874 " pdb=" O2' G A 877 " model vdw 2.027 2.440 nonbonded pdb=" OG SER O 38 " pdb=" O HIS O 41 " model vdw 2.031 2.440 nonbonded pdb=" O2' U A1334 " pdb=" OH TYR E 192 " model vdw 2.046 2.440 nonbonded pdb=" OG1 THR F 136 " pdb=" OD1 ASN F 162 " model vdw 2.070 2.440 ... (remaining 834869 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 3233 5.49 5 S 53 5.16 5 C 46406 2.51 5 N 17745 2.21 5 O 26869 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: 0.560 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: 0.080 Extract box with map and model: 9.500 Check model and map are aligned: 1.240 Convert atoms to be neutral: 0.780 Process input model: 323.450 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 339.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 0.122 102983 Z= 0.405 Angle : 0.904 9.891 155232 Z= 0.468 Chirality : 0.046 0.357 19969 Planarity : 0.008 0.103 7675 Dihedral : 11.169 179.807 48569 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.60 % Allowed : 10.20 % Favored : 89.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.14), residues: 3156 helix: -0.67 (0.17), residues: 770 sheet: -1.38 (0.21), residues: 552 loop : -1.93 (0.14), residues: 1834 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 883 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 883 average time/residue: 1.0632 time to fit residues: 1474.2432 Evaluate side-chains 636 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 636 time to evaluate : 3.838 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 532 optimal weight: 9.9990 chunk 478 optimal weight: 6.9990 chunk 265 optimal weight: 50.0000 chunk 163 optimal weight: 8.9990 chunk 322 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 494 optimal weight: 0.0770 chunk 191 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 368 optimal weight: 7.9990 chunk 573 optimal weight: 5.9990 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS ** 1 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 53 ASN 3 63 ASN C 76 ASN C 227 ASN C 233 HIS D 51 GLN D 135 GLN D 145 HIS D 183 HIS E 182 HIS G 7 GLN G 144 GLN J 147 GLN K 4 GLN M 17 GLN M 123 HIS O 36 HIS ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN Q 77 ASN Q 94 ASN R 68 HIS R 93 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 58 HIS V 62 ASN V 74 GLN ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 102983 Z= 0.359 Angle : 0.734 11.399 155232 Z= 0.368 Chirality : 0.039 0.341 19969 Planarity : 0.006 0.062 7675 Dihedral : 12.886 178.159 42406 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.29 % Favored : 92.43 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.94 (0.14), residues: 3156 helix: -0.02 (0.18), residues: 765 sheet: -1.24 (0.21), residues: 533 loop : -1.92 (0.13), residues: 1858 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 796 time to evaluate : 4.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 90 outliers final: 53 residues processed: 827 average time/residue: 1.0019 time to fit residues: 1341.0510 Evaluate side-chains 750 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 697 time to evaluate : 3.842 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.7074 time to fit residues: 73.4220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 318 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 476 optimal weight: 9.9990 chunk 390 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 574 optimal weight: 0.9980 chunk 620 optimal weight: 6.9990 chunk 511 optimal weight: 2.9990 chunk 569 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 460 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 HIS 1 44 ASN 1 51 HIS C 76 ASN D 135 GLN D 139 HIS D 179 ASN D 183 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 ASN M 123 HIS N 23 ASN ** O 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 HIS R 89 GLN ** S 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN W 29 GLN X 32 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 102983 Z= 0.207 Angle : 0.567 10.576 155232 Z= 0.290 Chirality : 0.033 0.333 19969 Planarity : 0.005 0.060 7675 Dihedral : 12.835 179.909 42406 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.67 % Favored : 92.08 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3156 helix: 0.26 (0.19), residues: 774 sheet: -1.14 (0.21), residues: 544 loop : -1.91 (0.14), residues: 1838 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 763 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 43 residues processed: 789 average time/residue: 1.0208 time to fit residues: 1320.7804 Evaluate side-chains 760 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 717 time to evaluate : 3.850 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.7416 time to fit residues: 63.4874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 567 optimal weight: 0.0000 chunk 431 optimal weight: 30.0000 chunk 297 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 385 optimal weight: 6.9990 chunk 576 optimal weight: 2.9990 chunk 609 optimal weight: 0.7980 chunk 300 optimal weight: 10.0000 chunk 546 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 overall best weight: 3.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 183 HIS ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 ASN M 123 HIS O 118 ASN R 68 HIS S 71 ASN ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 HIS W 29 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 102983 Z= 0.207 Angle : 0.562 10.763 155232 Z= 0.288 Chirality : 0.033 0.342 19969 Planarity : 0.005 0.089 7675 Dihedral : 12.988 178.877 42406 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.32 % Favored : 92.43 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3156 helix: 0.36 (0.19), residues: 772 sheet: -1.08 (0.22), residues: 509 loop : -1.90 (0.13), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 748 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 45 residues processed: 771 average time/residue: 0.9905 time to fit residues: 1249.3158 Evaluate side-chains 769 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 724 time to evaluate : 3.977 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.7164 time to fit residues: 64.3350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 507 optimal weight: 4.9990 chunk 346 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 454 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 520 optimal weight: 0.9990 chunk 421 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 547 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS N 62 ASN Q 66 ASN R 68 HIS ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 102983 Z= 0.297 Angle : 0.633 11.167 155232 Z= 0.320 Chirality : 0.036 0.374 19969 Planarity : 0.005 0.069 7675 Dihedral : 13.369 178.809 42406 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.59 % Favored : 91.16 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.88 (0.14), residues: 3156 helix: 0.20 (0.19), residues: 766 sheet: -1.06 (0.22), residues: 504 loop : -2.02 (0.13), residues: 1886 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 754 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 50 residues processed: 780 average time/residue: 0.9872 time to fit residues: 1263.4774 Evaluate side-chains 766 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 716 time to evaluate : 3.809 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.7022 time to fit residues: 70.8349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 205 optimal weight: 10.0000 chunk 549 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 358 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 610 optimal weight: 8.9990 chunk 506 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 320 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS C 76 ASN D 183 HIS ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 ASN M 123 HIS ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 HIS R 91 HIS ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 GLN U 25 GLN V 91 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 102983 Z= 0.386 Angle : 0.730 13.441 155232 Z= 0.366 Chirality : 0.039 0.414 19969 Planarity : 0.006 0.101 7675 Dihedral : 13.947 178.818 42406 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.92 % Favored : 89.83 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.24 (0.14), residues: 3156 helix: -0.17 (0.19), residues: 757 sheet: -1.13 (0.22), residues: 523 loop : -2.26 (0.13), residues: 1876 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 756 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 57 residues processed: 783 average time/residue: 1.0583 time to fit residues: 1354.3580 Evaluate side-chains 781 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 724 time to evaluate : 3.876 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.7652 time to fit residues: 85.1359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 588 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 347 optimal weight: 20.0000 chunk 445 optimal weight: 10.0000 chunk 345 optimal weight: 10.0000 chunk 513 optimal weight: 8.9990 chunk 340 optimal weight: 20.0000 chunk 608 optimal weight: 10.0000 chunk 380 optimal weight: 6.9990 chunk 370 optimal weight: 0.8980 chunk 280 optimal weight: 10.0000 overall best weight: 7.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 20 ASN C 76 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 ASN M 123 HIS ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 GLN ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.092 102983 Z= 0.403 Angle : 0.744 13.510 155232 Z= 0.372 Chirality : 0.040 0.450 19969 Planarity : 0.006 0.084 7675 Dihedral : 14.223 179.127 42406 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.30 % Favored : 89.45 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.14), residues: 3156 helix: -0.31 (0.18), residues: 760 sheet: -1.23 (0.22), residues: 514 loop : -2.34 (0.13), residues: 1882 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 740 time to evaluate : 4.019 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 outliers start: 67 outliers final: 46 residues processed: 760 average time/residue: 0.9979 time to fit residues: 1240.4383 Evaluate side-chains 755 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 709 time to evaluate : 3.841 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.6995 time to fit residues: 64.6793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 376 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 363 optimal weight: 2.9990 chunk 183 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 386 optimal weight: 1.9990 chunk 414 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 478 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 20 ASN C 76 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN M 123 HIS R 68 HIS ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 102983 Z= 0.278 Angle : 0.636 10.307 155232 Z= 0.325 Chirality : 0.036 0.414 19969 Planarity : 0.005 0.079 7675 Dihedral : 14.080 179.401 42406 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.22 % Favored : 90.59 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.21 (0.14), residues: 3156 helix: -0.11 (0.19), residues: 757 sheet: -1.19 (0.22), residues: 515 loop : -2.23 (0.13), residues: 1884 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 739 time to evaluate : 3.873 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: 38 outliers final: 28 residues processed: 750 average time/residue: 1.0644 time to fit residues: 1311.4657 Evaluate side-chains 744 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 716 time to evaluate : 3.829 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6917 time to fit residues: 41.1490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 553 optimal weight: 0.9980 chunk 582 optimal weight: 0.8980 chunk 531 optimal weight: 6.9990 chunk 566 optimal weight: 0.9990 chunk 341 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 445 optimal weight: 0.3980 chunk 173 optimal weight: 10.0000 chunk 512 optimal weight: 7.9990 chunk 536 optimal weight: 5.9990 chunk 564 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN 3 31 HIS C 76 ASN D 139 HIS D 179 ASN D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS N 62 ASN R 68 HIS ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 71 ASN ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 GLN V 154 GLN V 178 ASN ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 102983 Z= 0.148 Angle : 0.528 10.230 155232 Z= 0.270 Chirality : 0.031 0.338 19969 Planarity : 0.005 0.072 7675 Dihedral : 13.706 179.960 42406 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.83 % Favored : 92.05 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.15), residues: 3156 helix: 0.33 (0.20), residues: 753 sheet: -1.24 (0.21), residues: 555 loop : -2.02 (0.14), residues: 1848 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 755 time to evaluate : 3.872 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 outliers start: 24 outliers final: 13 residues processed: 761 average time/residue: 0.9923 time to fit residues: 1232.5439 Evaluate side-chains 731 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 718 time to evaluate : 3.861 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.6861 time to fit residues: 20.6918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 372 optimal weight: 5.9990 chunk 599 optimal weight: 10.0000 chunk 365 optimal weight: 3.9990 chunk 284 optimal weight: 10.0000 chunk 416 optimal weight: 20.0000 chunk 628 optimal weight: 8.9990 chunk 578 optimal weight: 9.9990 chunk 500 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN 6 20 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 183 HIS ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 71 ASN ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 102983 Z= 0.392 Angle : 0.718 10.099 155232 Z= 0.358 Chirality : 0.039 0.426 19969 Planarity : 0.006 0.082 7675 Dihedral : 14.167 177.425 42406 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.52 % Favored : 89.32 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.23 (0.14), residues: 3156 helix: -0.10 (0.19), residues: 761 sheet: -1.27 (0.22), residues: 503 loop : -2.23 (0.13), residues: 1892 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 718 time to evaluate : 3.895 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: 22 outliers final: 18 residues processed: 722 average time/residue: 1.0051 time to fit residues: 1184.9705 Evaluate side-chains 727 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 709 time to evaluate : 3.890 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.6797 time to fit residues: 27.3011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 397 optimal weight: 10.0000 chunk 533 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 461 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 501 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 514 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 20 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS J 132 HIS K 51 ASN L 126 HIS M 123 HIS ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 HIS ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122727 restraints weight = 174269.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123634 restraints weight = 93177.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123763 restraints weight = 80265.029| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 102983 Z= 0.423 Angle : 0.772 11.578 155232 Z= 0.385 Chirality : 0.041 0.448 19969 Planarity : 0.006 0.077 7675 Dihedral : 14.632 178.548 42406 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.38 % Favored : 88.47 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.55 (0.14), residues: 3156 helix: -0.52 (0.18), residues: 764 sheet: -1.48 (0.22), residues: 498 loop : -2.36 (0.13), residues: 1894 =============================================================================== Job complete usr+sys time: 18326.11 seconds wall clock time: 326 minutes 20.25 seconds (19580.25 seconds total)