Starting phenix.real_space_refine (version: dev) on Fri Dec 16 12:11:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/12_2022/6dzk_8934.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/12_2022/6dzk_8934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/12_2022/6dzk_8934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/12_2022/6dzk_8934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/12_2022/6dzk_8934.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/12_2022/6dzk_8934.pdb" } resolution = 3.6 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= 0.000 sd= 0.004 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 "C ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 90307 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 48753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1511, 48753 Classifications: {'RNA': 1511} Modifications used: {'3*END': 1, 'rna2p_pur': 113, 'rna2p_pyr': 86, 'rna3p_pur': 736, 'rna3p_pyr': 576} Link IDs: {'rna2p': 199, 'rna3p': 1311} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 622 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3367 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3309 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "E" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2656 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain: "F" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1568 Classifications: {'peptide': 96} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "G" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2514 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "H" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2056 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "I" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2044 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "J" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1607 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "K" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1718 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "M" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1921 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "O" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1480 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "P" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1826 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "Q" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1543 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "S" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1339 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1372 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "V" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3632 Classifications: {'peptide': 228} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "r" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1375 Classifications: {'peptide': 84} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Y" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1720 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "N" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1685 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "g" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 197 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Time building chain proxies: 33.34, per 1000 atoms: 0.37 Number of scatterers: 90307 At special positions: 0 Unit cell: (204.37, 207.58, 180.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 1511 15.00 O 14173 8.00 N 9897 7.00 C 27144 6.00 H 37538 1.00 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: 63.39 Conformation dependent library (CDL) restraints added in 3.5 seconds 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4746 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 25 sheets defined 45.1% alpha, 15.4% beta 466 base pairs and 780 stacking pairs defined. Time for finding SS restraints: 34.12 Creating SS restraints... Processing helix chain 'B' and resid 4 through 30 removed outlier: 5.477A pdb=" N VAL B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG B 29 " --> pdb=" O ARG B 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 126 removed outlier: 4.038A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 Processing helix chain 'D' and resid 7 through 15 removed outlier: 4.174A pdb=" N LYS D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 29 Processing helix chain 'D' and resid 44 through 61 removed outlier: 3.791A pdb=" N GLN D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.817A 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 101 Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 142 through 145 removed outlier: 4.189A pdb=" N LEU D 145 " --> pdb=" O GLU D 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 145' Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'E' and resid 80 through 95 Processing helix chain 'E' and resid 134 through 144 Processing helix chain 'E' and resid 157 through 172 Processing helix chain 'E' and resid 174 through 182 Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'E' and resid 191 through 213 removed outlier: 4.101A pdb=" N LEU E 195 " --> pdb=" O PRO E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 35 removed outlier: 4.682A pdb=" N ALA F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Proline residue: F 21 - end of helix removed outlier: 4.146A pdb=" N PHE F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL F 29 " --> pdb=" O THR F 25 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE F 30 " --> pdb=" O PHE F 26 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP F 33 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 82 Processing helix chain 'G' and resid 20 through 31 removed outlier: 4.276A 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: 4.373A pdb=" N THR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 149 through 152 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.942A pdb=" N LEU H 94 " --> pdb=" O SER H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 removed outlier: 3.597A pdb=" N LEU H 101 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'I' and resid 61 through 76 Proline residue: I 71 - end of helix Processing helix chain 'I' and resid 91 through 111 Processing helix chain 'I' and resid 112 through 118 Proline residue: I 116 - end of helix Processing helix chain 'J' and resid 14 through 32 removed outlier: 3.985A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 88 Processing helix chain 'K' and resid 56 through 60 Processing helix chain 'K' and resid 68 through 87 removed outlier: 3.721A pdb=" N ALA K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'M' and resid 14 through 19 Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 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 Processing helix chain 'O' and resid 4 through 15 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.037A pdb=" N VAL O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.051A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 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 'S' and resid 12 through 25 Processing helix chain 'S' and resid 41 through 45 removed outlier: 3.505A pdb=" N PHE S 44 " --> pdb=" O ILE S 41 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.508A pdb=" N MET S 66 " --> pdb=" O THR S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 74 Processing helix chain 'T' and resid 4 through 42 Processing helix chain 'T' and resid 43 through 64 removed outlier: 4.125A pdb=" N ALA T 53 " --> pdb=" O GLU T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 86 Processing helix chain 'V' and resid 5 through 12 removed outlier: 4.041A pdb=" N SER V 12 " --> pdb=" O GLN V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 64 Processing helix chain 'V' and resid 76 through 88 Processing helix chain 'V' and resid 103 through 124 removed outlier: 3.706A pdb=" N VAL V 107 " --> pdb=" O ASN V 103 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS V 109 " --> pdb=" O SER V 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 148 Processing helix chain 'V' and resid 169 through 172 Processing helix chain 'V' and resid 173 through 178 Processing helix chain 'V' and resid 192 through 196 removed outlier: 3.969A pdb=" N VAL V 195 " --> pdb=" O ASP V 192 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL V 196 " --> pdb=" O PRO V 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 192 through 196' Processing helix chain 'V' and resid 206 through 227 Processing helix chain 'r' and resid 22 through 27 Processing helix chain 'r' and resid 36 through 41 removed outlier: 3.511A pdb=" N LEU r 40 " --> pdb=" O ASP r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 44 No H-bonds generated for 'chain 'r' and resid 42 through 44' Processing helix chain 'r' and resid 59 through 76 Processing helix chain 'Y' and resid 17 through 33 removed outlier: 3.849A pdb=" N ARG Y 21 " --> pdb=" O PRO Y 17 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR Y 22 " --> pdb=" O ASP Y 18 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU Y 31 " --> pdb=" O LYS Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 102 removed outlier: 3.567A pdb=" N ALA Y 83 " --> pdb=" O SER Y 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 26 through 33 Processing helix chain 'N' and resid 43 through 51 Processing helix chain 'N' and resid 52 through 56 removed outlier: 3.662A pdb=" N SER N 55 " --> pdb=" O PRO N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 Processing helix chain 'g' and resid 73 through 81 Processing sheet with id=AA1, first strand: chain 'C' and resid 54 through 55 removed outlier: 7.651A pdb=" N VAL C 63 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN C 101 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE C 67 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.568A pdb=" N GLY C 148 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE C 196 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA C 189 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 204 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.996A pdb=" N VAL D 125 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE D 118 " --> pdb=" O VAL D 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.864A pdb=" N LYS E 48 " --> pdb=" O ARG E 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AA6, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 110 through 113 removed outlier: 3.639A pdb=" N ARG E 122 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 110 through 113 removed outlier: 6.226A pdb=" N VAL E 118 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 39 through 42 removed outlier: 3.757A pdb=" N ILE F 9 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 87 " --> pdb=" O ILE F 9 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 46 through 47 Processing sheet with id=AB2, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AB3, first strand: chain 'H' and resid 24 through 27 Processing sheet with id=AB4, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.636A pdb=" N ILE H 105 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR H 130 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL H 103 " --> pdb=" O TYR H 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 28 through 31 removed outlier: 6.593A pdb=" N ASN I 49 " --> pdb=" O ALA I 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 28 through 31 Processing sheet with id=AB7, first strand: chain 'J' and resid 35 through 41 removed outlier: 5.238A pdb=" N VAL J 36 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU J 77 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN J 47 " --> pdb=" O MET J 67 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 35 through 41 removed outlier: 5.238A pdb=" N VAL J 36 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU J 77 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE J 8 " --> pdb=" O ILE J 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 51 through 52 removed outlier: 3.794A pdb=" N GLU J 63 " --> pdb=" O VAL J 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 50 through 55 removed outlier: 4.141A pdb=" N ALA K 52 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA K 54 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL K 41 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.636A pdb=" N ALA L 65 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG L 54 " --> pdb=" O ARG L 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N CYS L 34 " --> pdb=" O LYS L 56 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG L 30 " --> pdb=" O VAL L 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 3 through 8 removed outlier: 3.758A pdb=" N TYR P 40 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY P 38 " --> pdb=" O ILE P 20 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU P 48 " --> pdb=" O HIS P 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 22 through 29 removed outlier: 15.400A pdb=" N THR Q 22 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) removed outlier: 11.828A pdb=" N ARG Q 43 " --> pdb=" O THR Q 22 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE Q 24 " --> pdb=" O GLU Q 41 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU Q 41 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR Q 26 " --> pdb=" O GLU Q 39 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL Q 37 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP Q 42 " --> pdb=" O THR Q 55 " (cutoff:3.500A) removed outlier: 16.691A pdb=" N LYS Q 86 " --> pdb=" O THR Q 56 " (cutoff:3.500A) removed outlier: 14.149A pdb=" N LYS Q 58 " --> pdb=" O LYS Q 86 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N TRP Q 88 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS Q 60 " --> pdb=" O TRP Q 88 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LEU Q 90 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N HIS Q 62 " --> pdb=" O LEU Q 90 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N GLU Q 92 " --> pdb=" O HIS Q 62 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG Q 87 " --> pdb=" O THR Q 79 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL Q 91 " --> pdb=" O SER Q 75 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER Q 75 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE Q 93 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ARG Q 73 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY Q 25 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA Q 23 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 30 through 32 removed outlier: 6.589A pdb=" N ILE S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N HIS S 52 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 41 through 43 Processing sheet with id=AC7, first strand: chain 'Y' and resid 41 through 43 962 hydrogen bonds defined for protein. 2787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1199 hydrogen bonds 1958 hydrogen bond angles 0 basepair planarities 466 basepair parallelities 780 stacking parallelities Total time for adding SS restraints: 48.93 Time building geometry restraints manager: 66.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 37529 1.03 - 1.22: 328 1.22 - 1.42: 28234 1.42 - 1.61: 28306 1.61 - 1.81: 84 Bond restraints: 94481 Sorted by residual: bond pdb=" CA PRO I 128 " pdb=" CB PRO I 128 " ideal model delta sigma weight residual 1.531 1.558 -0.027 6.20e-03 2.60e+04 1.87e+01 bond pdb=" CA ILE C 56 " pdb=" CB ILE C 56 " ideal model delta sigma weight residual 1.540 1.592 -0.052 1.36e-02 5.41e+03 1.46e+01 bond pdb=" NZ LYS Y 10 " pdb=" HZ3 LYS Y 10 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS Y 10 " pdb=" HZ1 LYS Y 10 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" NZ LYS Y 10 " pdb=" HZ2 LYS Y 10 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 94476 not shown) Histogram of bond angle deviations from ideal: 60.08 - 76.65: 208 76.65 - 93.22: 187 93.22 - 109.79: 72194 109.79 - 126.36: 92763 126.36 - 142.93: 4658 Bond angle restraints: 170010 Sorted by residual: angle pdb=" C MET C 133 " pdb=" N ARG C 134 " pdb=" H ARG C 134 " ideal model delta sigma weight residual 124.96 69.53 55.43 3.00e+00 1.11e-01 3.41e+02 angle pdb=" C SER V 79 " pdb=" N ILE V 80 " pdb=" H ILE V 80 " ideal model delta sigma weight residual 124.92 69.80 55.12 3.00e+00 1.11e-01 3.38e+02 angle pdb=" C ALA V 218 " pdb=" N SER V 219 " pdb=" H SER V 219 " ideal model delta sigma weight residual 125.01 70.14 54.87 3.00e+00 1.11e-01 3.34e+02 angle pdb=" CA ARG C 134 " pdb=" N ARG C 134 " pdb=" H ARG C 134 " ideal model delta sigma weight residual 114.66 60.08 54.58 3.00e+00 1.11e-01 3.31e+02 angle pdb=" CA SER V 219 " pdb=" N SER V 219 " pdb=" H SER V 219 " ideal model delta sigma weight residual 114.71 60.14 54.57 3.00e+00 1.11e-01 3.31e+02 ... (remaining 170005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 34715 35.81 - 71.62: 2243 71.62 - 107.44: 363 107.44 - 143.25: 26 143.25 - 179.06: 25 Dihedral angle restraints: 37372 sinusoidal: 29213 harmonic: 8159 Sorted by residual: dihedral pdb=" CA ILE C 56 " pdb=" C ILE C 56 " pdb=" N GLU C 57 " pdb=" CA GLU C 57 " ideal model delta harmonic sigma weight residual -180.00 -126.85 -53.15 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA GLY C 158 " pdb=" C GLY C 158 " pdb=" N GLY C 159 " pdb=" CA GLY C 159 " ideal model delta harmonic sigma weight residual -180.00 -128.74 -51.26 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" C5' A A1339 " pdb=" C4' A A1339 " pdb=" C3' A A1339 " pdb=" O3' A A1339 " ideal model delta sinusoidal sigma weight residual 147.00 77.50 69.50 1 8.00e+00 1.56e-02 9.75e+01 ... (remaining 37369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.364: 10573 0.364 - 0.728: 28 0.728 - 1.091: 16 1.091 - 1.455: 6 1.455 - 1.819: 24 Chirality restraints: 10647 Sorted by residual: chirality pdb=" CG LEU L 7 " pdb=" CB LEU L 7 " pdb=" CD1 LEU L 7 " pdb=" CD2 LEU L 7 " both_signs ideal model delta sigma weight residual False -2.59 -0.77 -1.82 2.00e-01 2.50e+01 8.27e+01 chirality pdb=" CG LEU C 90 " pdb=" CB LEU C 90 " pdb=" CD1 LEU C 90 " pdb=" CD2 LEU C 90 " both_signs ideal model delta sigma weight residual False -2.59 -0.79 -1.80 2.00e-01 2.50e+01 8.08e+01 chirality pdb=" CG LEU C 42 " pdb=" CB LEU C 42 " pdb=" CD1 LEU C 42 " pdb=" CD2 LEU C 42 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 8.03e+01 ... (remaining 10644 not shown) Planarity restraints: 8752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 670 " 0.052 2.00e-02 2.50e+03 2.09e-02 1.53e+01 pdb=" N9 G A 670 " -0.055 2.00e-02 2.50e+03 pdb=" C8 G A 670 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G A 670 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A 670 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G A 670 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 670 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A 670 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G A 670 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G A 670 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 670 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 670 " -0.006 2.00e-02 2.50e+03 pdb=" H8 G A 670 " -0.003 2.00e-02 2.50e+03 pdb=" H1 G A 670 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 298 " -0.052 2.00e-02 2.50e+03 2.12e-02 1.46e+01 pdb=" N9 A A 298 " 0.050 2.00e-02 2.50e+03 pdb=" C8 A A 298 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A A 298 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A 298 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A 298 " -0.023 2.00e-02 2.50e+03 pdb=" N1 A A 298 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A A 298 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 298 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 298 " 0.004 2.00e-02 2.50e+03 pdb=" H8 A A 298 " 0.002 2.00e-02 2.50e+03 pdb=" H2 A A 298 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 985 " 0.046 2.00e-02 2.50e+03 1.93e-02 1.30e+01 pdb=" N9 G A 985 " -0.045 2.00e-02 2.50e+03 pdb=" C8 G A 985 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 985 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 985 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 985 " 0.022 2.00e-02 2.50e+03 pdb=" O6 G A 985 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G A 985 " -0.015 2.00e-02 2.50e+03 pdb=" C2 G A 985 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G A 985 " -0.009 2.00e-02 2.50e+03 pdb=" N3 G A 985 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 985 " -0.003 2.00e-02 2.50e+03 pdb=" H8 G A 985 " -0.007 2.00e-02 2.50e+03 pdb=" H1 G A 985 " 0.008 2.00e-02 2.50e+03 ... (remaining 8749 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 3392 2.16 - 2.77: 145166 2.77 - 3.38: 230203 3.38 - 3.99: 319598 3.99 - 4.60: 485232 Nonbonded interactions: 1183591 Sorted by model distance: nonbonded pdb=" H GLU C 166 " pdb=" HA GLU C 166 " model vdw 1.545 1.816 nonbonded pdb=" H LEU V 179 " pdb=" HA LEU V 179 " model vdw 1.557 1.816 nonbonded pdb=" H ALA V 160 " pdb=" HA ALA V 160 " model vdw 1.564 1.816 nonbonded pdb=" H ASP V 188 " pdb=" HA ASP V 188 " model vdw 1.587 1.816 nonbonded pdb=" H VAL V 164 " pdb=" HA VAL V 164 " model vdw 1.587 1.816 ... (remaining 1183586 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: 6 Type Number sf(0) Gaussians P 1511 5.49 5 S 44 5.16 5 C 27144 2.51 5 N 9897 2.21 5 O 14173 1.98 5 H 37538 0.53 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: 6.730 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: 0.850 Extract box with map and model: 23.830 Check model and map are aligned: 1.090 Convert atoms to be neutral: 0.600 Process input model: 266.430 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.200 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 303.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.008 0.085 56943 Z= 0.466 Angle : 1.009 22.062 84385 Z= 0.531 Chirality : 0.106 1.819 10647 Planarity : 0.006 0.079 5108 Dihedral : 15.338 179.060 26245 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.79 % Favored : 89.94 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.80 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.49 % 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: -4.16 (0.14), residues: 2524 helix: -1.79 (0.13), residues: 1076 sheet: -3.36 (0.21), residues: 398 loop : -3.49 (0.17), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 847 time to evaluate : 3.885 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 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 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: 2 outliers final: 2 residues processed: 849 average time/residue: 1.3714 time to fit residues: 1759.0409 Evaluate side-chains 503 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 501 time to evaluate : 3.922 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7600 time to fit residues: 6.8479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 312 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 362 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 178 HIS D 185 GLN F 96 HIS G 68 ASN G 106 ASN G 148 ASN H 63 GLN H 121 GLN I 80 GLN J 47 ASN L 6 GLN L 29 GLN S 57 HIS S 69 HIS T 14 ASN ** V 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 56943 Z= 0.254 Angle : 0.784 18.079 84385 Z= 0.410 Chirality : 0.101 1.781 10647 Planarity : 0.006 0.068 5108 Dihedral : 16.291 179.987 21035 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.23 % Favored : 90.65 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.16), residues: 2524 helix: -0.25 (0.15), residues: 1084 sheet: -2.66 (0.23), residues: 397 loop : -3.07 (0.18), residues: 1043 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 556 time to evaluate : 3.919 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 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 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: 49 outliers final: 37 residues processed: 586 average time/residue: 1.2193 time to fit residues: 1125.8797 Evaluate side-chains 525 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 488 time to evaluate : 3.926 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 4 residues processed: 37 average time/residue: 0.8081 time to fit residues: 59.4672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 0.0010 chunk 112 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 362 optimal weight: 6.9990 chunk 392 optimal weight: 4.9990 chunk 323 optimal weight: 0.3980 chunk 359 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 overall best weight: 2.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 GLN G 68 ASN G 148 ASN H 121 GLN I 47 GLN M 63 ASN V 77 GLN V 167 ASN V 190 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 56943 Z= 0.312 Angle : 0.784 18.477 84385 Z= 0.413 Chirality : 0.102 1.894 10647 Planarity : 0.006 0.068 5108 Dihedral : 16.443 177.858 21035 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.18 % Favored : 89.74 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 (0.16), residues: 2524 helix: 0.25 (0.15), residues: 1084 sheet: -2.41 (0.24), residues: 402 loop : -2.98 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 521 time to evaluate : 3.920 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 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: 51 outliers final: 38 residues processed: 544 average time/residue: 1.2182 time to fit residues: 1048.8523 Evaluate side-chains 497 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 459 time to evaluate : 3.926 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 3 residues processed: 38 average time/residue: 0.8877 time to fit residues: 63.2609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 7.9990 chunk 272 optimal weight: 0.8980 chunk 188 optimal weight: 0.2980 chunk 40 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 364 optimal weight: 4.9990 chunk 385 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 345 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS G 68 ASN H 121 GLN V 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 56943 Z= 0.185 Angle : 0.704 18.424 84385 Z= 0.374 Chirality : 0.100 1.727 10647 Planarity : 0.004 0.063 5108 Dihedral : 16.145 179.918 21035 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.88 % Favored : 92.08 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.57 (0.17), residues: 2524 helix: 0.89 (0.16), residues: 1063 sheet: -2.16 (0.24), residues: 412 loop : -2.66 (0.18), residues: 1049 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 498 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 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 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: 25 outliers final: 19 residues processed: 511 average time/residue: 1.1691 time to fit residues: 947.5574 Evaluate side-chains 476 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 457 time to evaluate : 3.912 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.8654 time to fit residues: 33.2807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 0.9990 chunk 218 optimal weight: 0.0030 chunk 5 optimal weight: 3.9990 chunk 287 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 329 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN G 68 ASN G 129 ASN H 121 GLN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 77 GLN V 190 ASN ** r 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 56943 Z= 0.218 Angle : 0.703 18.533 84385 Z= 0.374 Chirality : 0.100 1.824 10647 Planarity : 0.005 0.058 5108 Dihedral : 16.095 178.406 21035 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.27 % Favored : 90.69 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.30 (0.17), residues: 2524 helix: 1.13 (0.16), residues: 1064 sheet: -1.99 (0.25), residues: 394 loop : -2.55 (0.18), residues: 1066 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 492 time to evaluate : 3.905 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 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: 32 outliers final: 25 residues processed: 502 average time/residue: 1.1360 time to fit residues: 907.8198 Evaluate side-chains 488 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 463 time to evaluate : 3.891 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 5 residues processed: 25 average time/residue: 0.8948 time to fit residues: 43.0883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 129 optimal weight: 6.9990 chunk 347 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 320 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN F 96 HIS G 25 GLN G 68 ASN G 148 ASN H 121 GLN M 63 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 190 ASN N 10 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 56943 Z= 0.322 Angle : 0.763 18.619 84385 Z= 0.403 Chirality : 0.102 1.850 10647 Planarity : 0.005 0.060 5108 Dihedral : 16.417 177.148 21035 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.58 % Favored : 89.38 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.49 (0.17), residues: 2524 helix: 0.86 (0.16), residues: 1067 sheet: -2.08 (0.25), residues: 401 loop : -2.54 (0.18), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 475 time to evaluate : 3.945 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 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: 46 outliers final: 35 residues processed: 493 average time/residue: 1.1585 time to fit residues: 905.2690 Evaluate side-chains 493 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 458 time to evaluate : 3.930 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 6 residues processed: 35 average time/residue: 0.7795 time to fit residues: 54.1317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 324 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 384 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN D 115 HIS D 167 GLN G 25 GLN G 68 ASN G 148 ASN M 63 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 190 ASN ** r 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 56943 Z= 0.225 Angle : 0.704 18.404 84385 Z= 0.375 Chirality : 0.100 1.792 10647 Planarity : 0.005 0.058 5108 Dihedral : 16.166 177.569 21035 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.40 % Favored : 91.56 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.20 (0.17), residues: 2524 helix: 1.13 (0.16), residues: 1067 sheet: -1.91 (0.25), residues: 391 loop : -2.43 (0.18), residues: 1066 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 492 time to evaluate : 3.967 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 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: 18 outliers final: 15 residues processed: 504 average time/residue: 1.1130 time to fit residues: 893.1486 Evaluate side-chains 480 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 465 time to evaluate : 3.936 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 15 average time/residue: 0.8027 time to fit residues: 25.6456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 237 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 25 GLN G 148 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 190 ASN N 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 56943 Z= 0.333 Angle : 0.762 18.510 84385 Z= 0.401 Chirality : 0.102 1.869 10647 Planarity : 0.005 0.065 5108 Dihedral : 16.394 177.147 21035 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.74 % Favored : 89.22 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2524 helix: 0.93 (0.16), residues: 1067 sheet: -1.96 (0.25), residues: 399 loop : -2.46 (0.19), residues: 1058 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 474 time to evaluate : 4.021 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 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: 25 outliers final: 19 residues processed: 484 average time/residue: 1.1359 time to fit residues: 875.0986 Evaluate side-chains 479 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 460 time to evaluate : 3.948 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 19 average time/residue: 0.7986 time to fit residues: 32.0766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 349 optimal weight: 10.0000 chunk 368 optimal weight: 0.9990 chunk 336 optimal weight: 3.9990 chunk 358 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 281 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 323 optimal weight: 0.6980 chunk 338 optimal weight: 6.9990 chunk 357 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN G 148 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 56943 Z= 0.198 Angle : 0.696 18.320 84385 Z= 0.371 Chirality : 0.100 1.812 10647 Planarity : 0.004 0.059 5108 Dihedral : 16.132 177.506 21035 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.92 % Favored : 92.04 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.06 (0.17), residues: 2524 helix: 1.22 (0.16), residues: 1065 sheet: -1.82 (0.25), residues: 403 loop : -2.31 (0.19), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 483 time to evaluate : 3.984 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 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: 18 outliers final: 14 residues processed: 490 average time/residue: 1.1140 time to fit residues: 870.6026 Evaluate side-chains 477 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 463 time to evaluate : 3.877 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 14 average time/residue: 0.8117 time to fit residues: 24.5911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 235 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 397 optimal weight: 4.9990 chunk 365 optimal weight: 5.9990 chunk 316 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 167 GLN G 148 ASN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 56943 Z= 0.233 Angle : 0.705 18.388 84385 Z= 0.376 Chirality : 0.100 1.824 10647 Planarity : 0.005 0.060 5108 Dihedral : 16.133 177.336 21035 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.71 % Favored : 90.25 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.02 (0.17), residues: 2524 helix: 1.23 (0.16), residues: 1065 sheet: -1.73 (0.25), residues: 399 loop : -2.29 (0.19), residues: 1060 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5048 Ramachandran restraints generated. 2524 Oldfield, 0 Emsley, 2524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 471 time to evaluate : 4.023 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 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: 19 outliers final: 13 residues processed: 479 average time/residue: 1.1192 time to fit residues: 856.1591 Evaluate side-chains 463 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 450 time to evaluate : 3.892 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 13 average time/residue: 0.8003 time to fit residues: 22.8944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 251 optimal weight: 4.9990 chunk 337 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 317 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 325 optimal weight: 0.4980 chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 167 GLN G 68 ASN G 148 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083276 restraints weight = 384214.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.085374 restraints weight = 133914.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086584 restraints weight = 78334.115| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 56943 Z= 0.336 Angle : 0.761 18.436 84385 Z= 0.401 Chirality : 0.102 1.842 10647 Planarity : 0.005 0.061 5108 Dihedral : 16.366 177.294 21035 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.62 % Favored : 89.34 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 2524 helix: 0.97 (0.16), residues: 1065 sheet: -1.75 (0.26), residues: 391 loop : -2.38 (0.18), residues: 1068 =============================================================================== Job complete usr+sys time: 23782.20 seconds wall clock time: 411 minutes 14.44 seconds (24674.44 seconds total)