Starting phenix.real_space_refine on Tue Feb 20 19:58:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/02_2024/6dzk_8934.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/02_2024/6dzk_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_8934/02_2024/6dzk_8934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/02_2024/6dzk_8934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/02_2024/6dzk_8934.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzk_8934/02_2024/6dzk_8934.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 31.65, per 1000 atoms: 0.35 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: 66.95 Conformation dependent library (CDL) restraints added in 4.0 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: 36.11 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: 48.29 Time building geometry restraints manager: 69.66 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: 40401 35.81 - 71.62: 5346 71.62 - 107.44: 695 107.44 - 143.25: 26 143.25 - 179.06: 25 Dihedral angle restraints: 46493 sinusoidal: 38334 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 46490 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 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: 6.060 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: 1.020 Extract box with map and model: 21.650 Check model and map are aligned: 1.070 Set scattering table: 0.630 Process input model: 266.860 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 300.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 22.967 179.060 32019 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.79 % Favored : 89.94 % Rotamer: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 103 HIS 0.018 0.003 HIS K 127 PHE 0.024 0.004 PHE I 48 TYR 0.034 0.003 TYR P 40 ARG 0.016 0.002 ARG L 30 *********************** 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 : 3.952 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 REVERT: B 29 ARG cc_start: 0.7358 (mtt180) cc_final: 0.7018 (mtp-110) REVERT: C 81 THR cc_start: 0.5687 (m) cc_final: 0.5358 (p) REVERT: C 163 SER cc_start: 0.8625 (m) cc_final: 0.8236 (p) REVERT: C 183 ASP cc_start: 0.7276 (t0) cc_final: 0.6964 (t0) REVERT: D 144 SER cc_start: 0.6793 (p) cc_final: 0.5690 (t) REVERT: D 196 VAL cc_start: 0.9065 (t) cc_final: 0.8724 (p) REVERT: F 4 TYR cc_start: 0.7275 (m-80) cc_final: 0.6889 (m-80) REVERT: G 36 LYS cc_start: 0.7964 (tttt) cc_final: 0.7683 (tmtt) REVERT: I 51 ASP cc_start: 0.6459 (m-30) cc_final: 0.5252 (t0) REVERT: I 120 LYS cc_start: 0.8992 (tttt) cc_final: 0.8564 (tptm) REVERT: J 49 TYR cc_start: 0.7185 (m-80) cc_final: 0.6965 (m-80) REVERT: L 20 LYS cc_start: 0.8130 (mttt) cc_final: 0.7793 (mtpp) REVERT: L 21 THR cc_start: 0.7285 (m) cc_final: 0.7078 (p) REVERT: L 37 VAL cc_start: 0.8021 (t) cc_final: 0.7708 (m) REVERT: P 20 ILE cc_start: 0.9394 (mt) cc_final: 0.9133 (mt) REVERT: S 26 ASN cc_start: 0.7974 (m-40) cc_final: 0.7758 (m-40) REVERT: V 25 PRO cc_start: 0.5206 (Cg_exo) cc_final: 0.4979 (Cg_endo) REVERT: V 30 PHE cc_start: 0.4729 (m-80) cc_final: 0.4287 (m-10) REVERT: V 51 ASP cc_start: 0.7556 (t0) cc_final: 0.6807 (t0) REVERT: r 31 THR cc_start: 0.5330 (m) cc_final: 0.5046 (m) REVERT: Y 65 ARG cc_start: 0.6841 (mtm180) cc_final: 0.5739 (mtp85) outliers start: 2 outliers final: 2 residues processed: 849 average time/residue: 1.4837 time to fit residues: 1883.9509 Evaluate side-chains 511 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 509 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain Y residue 9 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 312 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 190 optimal weight: 0.7980 chunk 232 optimal weight: 4.9990 chunk 362 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN C 97 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN F 78 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 O 46 HIS S 47 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** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 56943 Z= 0.179 Angle : 0.760 18.294 84385 Z= 0.399 Chirality : 0.100 1.756 10647 Planarity : 0.005 0.069 5108 Dihedral : 24.431 179.918 26811 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.84 % Favored : 92.04 % Rotamer: Outliers : 1.82 % Allowed : 11.15 % Favored : 87.03 % 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: -0.31 (0.15), residues: 1095 sheet: -2.60 (0.23), residues: 405 loop : -3.05 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 162 HIS 0.007 0.001 HIS S 52 PHE 0.017 0.002 PHE Y 84 TYR 0.018 0.001 TYR P 40 ARG 0.008 0.001 ARG Q 73 *********************** 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 608 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 569 time to evaluate : 3.743 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: B 29 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6858 (mtp-110) REVERT: C 161 GLU cc_start: 0.5474 (pm20) cc_final: 0.5093 (pm20) REVERT: C 163 SER cc_start: 0.8606 (m) cc_final: 0.8406 (p) REVERT: C 183 ASP cc_start: 0.7333 (t0) cc_final: 0.6942 (t0) REVERT: F 7 MET cc_start: 0.8256 (ttm) cc_final: 0.7845 (ttm) REVERT: F 78 GLN cc_start: 0.7913 (pt0) cc_final: 0.7647 (pt0) REVERT: G 36 LYS cc_start: 0.8031 (tttt) cc_final: 0.7627 (tmtt) REVERT: G 106 ASN cc_start: 0.8476 (m-40) cc_final: 0.7652 (t0) REVERT: G 116 MET cc_start: 0.7520 (tpp) cc_final: 0.6979 (tpp) REVERT: I 51 ASP cc_start: 0.6422 (m-30) cc_final: 0.5087 (t0) REVERT: I 120 LYS cc_start: 0.9014 (tttt) cc_final: 0.8738 (tptt) REVERT: J 14 ASP cc_start: 0.8011 (t0) cc_final: 0.7234 (t0) REVERT: K 51 ILE cc_start: 0.8214 (pt) cc_final: 0.7948 (mp) REVERT: L 62 GLU cc_start: 0.7764 (tp30) cc_final: 0.7188 (tp30) REVERT: O 78 TYR cc_start: 0.8264 (t80) cc_final: 0.7988 (t80) REVERT: P 20 ILE cc_start: 0.9410 (mt) cc_final: 0.9193 (mt) REVERT: P 44 GLU cc_start: 0.7208 (mp0) cc_final: 0.6994 (mt-10) REVERT: S 26 ASN cc_start: 0.7948 (m-40) cc_final: 0.7718 (m-40) REVERT: V 83 GLU cc_start: 0.4769 (OUTLIER) cc_final: 0.4256 (tt0) REVERT: V 136 MET cc_start: 0.7931 (mmt) cc_final: 0.7726 (mmp) REVERT: V 208 ARG cc_start: 0.6803 (ttp-170) cc_final: 0.6602 (ttp-170) REVERT: r 31 THR cc_start: 0.4986 (m) cc_final: 0.4674 (m) REVERT: r 81 MET cc_start: 0.5712 (ppp) cc_final: 0.5418 (ppp) outliers start: 39 outliers final: 29 residues processed: 595 average time/residue: 1.3248 time to fit residues: 1225.9219 Evaluate side-chains 524 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 494 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 130 CYS Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 50 ILE Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 207 ILE Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain N residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 0.0000 chunk 112 optimal weight: 8.9990 chunk 301 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 362 optimal weight: 0.9980 chunk 392 optimal weight: 0.8980 chunk 323 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 HIS F 96 HIS G 68 ASN G 148 ASN I 47 GLN S 57 HIS S 69 HIS ** V 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 56943 Z= 0.234 Angle : 0.736 18.477 84385 Z= 0.390 Chirality : 0.100 1.814 10647 Planarity : 0.005 0.064 5108 Dihedral : 24.247 179.657 26811 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.23 % Favored : 90.69 % Rotamer: Outliers : 2.61 % Allowed : 12.65 % Favored : 84.74 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.91 (0.16), residues: 2524 helix: 0.54 (0.15), residues: 1074 sheet: -2.26 (0.24), residues: 403 loop : -2.84 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 162 HIS 0.035 0.001 HIS F 96 PHE 0.015 0.001 PHE V 16 TYR 0.014 0.001 TYR M 59 ARG 0.013 0.001 ARG Y 21 *********************** 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 588 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 532 time to evaluate : 3.726 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: C 161 GLU cc_start: 0.5838 (pm20) cc_final: 0.5315 (pm20) REVERT: C 183 ASP cc_start: 0.7364 (t0) cc_final: 0.7037 (t0) REVERT: F 72 VAL cc_start: 0.8835 (p) cc_final: 0.8507 (p) REVERT: F 76 ASP cc_start: 0.8250 (m-30) cc_final: 0.8014 (m-30) REVERT: G 36 LYS cc_start: 0.8024 (tttt) cc_final: 0.7639 (tmtt) REVERT: G 106 ASN cc_start: 0.8534 (m-40) cc_final: 0.7722 (t0) REVERT: G 116 MET cc_start: 0.7591 (tpp) cc_final: 0.7110 (tpp) REVERT: I 51 ASP cc_start: 0.6540 (m-30) cc_final: 0.5147 (t0) REVERT: I 83 ILE cc_start: 0.8870 (mp) cc_final: 0.8574 (mp) REVERT: I 120 LYS cc_start: 0.9138 (tttt) cc_final: 0.8841 (tptt) REVERT: K 45 ASP cc_start: 0.7397 (m-30) cc_final: 0.6951 (m-30) REVERT: K 51 ILE cc_start: 0.8320 (pt) cc_final: 0.8112 (mp) REVERT: P 8 THR cc_start: 0.9024 (t) cc_final: 0.8791 (p) REVERT: P 20 ILE cc_start: 0.9549 (mt) cc_final: 0.9308 (mt) REVERT: S 26 ASN cc_start: 0.7975 (m-40) cc_final: 0.7702 (m-40) REVERT: V 89 MET cc_start: 0.2315 (mmp) cc_final: 0.1764 (mtt) REVERT: r 31 THR cc_start: 0.4936 (m) cc_final: 0.4726 (m) REVERT: r 81 MET cc_start: 0.5902 (ppp) cc_final: 0.5570 (ppp) REVERT: N 98 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7858 (mtpp) outliers start: 56 outliers final: 45 residues processed: 565 average time/residue: 1.2655 time to fit residues: 1129.6410 Evaluate side-chains 528 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 483 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 130 CYS Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain V residue 38 ILE Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 161 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 207 ILE Chi-restraints excluded: chain r residue 54 HIS Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 chunk 385 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN G 129 ASN H 121 GLN V 77 GLN V 167 ASN V 190 ASN ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 56943 Z= 0.273 Angle : 0.749 18.515 84385 Z= 0.396 Chirality : 0.101 1.861 10647 Planarity : 0.005 0.066 5108 Dihedral : 24.225 178.265 26810 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.59 % Favored : 90.33 % Rotamer: Outliers : 3.59 % Allowed : 13.67 % Favored : 82.73 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.67 (0.17), residues: 2524 helix: 0.79 (0.16), residues: 1064 sheet: -2.11 (0.25), residues: 405 loop : -2.75 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 162 HIS 0.018 0.001 HIS F 96 PHE 0.021 0.002 PHE V 56 TYR 0.015 0.002 TYR M 59 ARG 0.007 0.001 ARG S 55 *********************** 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 591 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 514 time to evaluate : 3.837 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: B 24 THR cc_start: 0.9159 (m) cc_final: 0.8693 (p) REVERT: B 29 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7682 (mtp-110) REVERT: C 57 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: C 130 ARG cc_start: 0.6370 (mmt-90) cc_final: 0.5895 (mmt-90) REVERT: C 183 ASP cc_start: 0.7514 (t0) cc_final: 0.7282 (t0) REVERT: D 134 GLN cc_start: 0.7950 (mt0) cc_final: 0.7731 (mt0) REVERT: F 76 ASP cc_start: 0.8332 (m-30) cc_final: 0.7978 (m-30) REVERT: G 25 GLN cc_start: 0.7793 (tt0) cc_final: 0.7480 (tt0) REVERT: G 36 LYS cc_start: 0.8071 (tttt) cc_final: 0.7703 (tmtt) REVERT: G 106 ASN cc_start: 0.8394 (m-40) cc_final: 0.7861 (t0) REVERT: G 116 MET cc_start: 0.7568 (tpp) cc_final: 0.7111 (tpp) REVERT: I 51 ASP cc_start: 0.6659 (m-30) cc_final: 0.5232 (t0) REVERT: I 120 LYS cc_start: 0.9037 (tttt) cc_final: 0.8782 (tptt) REVERT: K 102 ARG cc_start: 0.6455 (mtp-110) cc_final: 0.6216 (mtp-110) REVERT: K 130 CYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8114 (t) REVERT: L 62 GLU cc_start: 0.7708 (tp30) cc_final: 0.7435 (tp30) REVERT: P 8 THR cc_start: 0.9119 (t) cc_final: 0.8772 (p) REVERT: P 20 ILE cc_start: 0.9599 (mt) cc_final: 0.9391 (mt) REVERT: S 26 ASN cc_start: 0.7966 (m-40) cc_final: 0.7662 (m-40) REVERT: V 89 MET cc_start: 0.2345 (mmp) cc_final: 0.1723 (mtt) REVERT: r 81 MET cc_start: 0.6007 (ppp) cc_final: 0.5752 (ppp) REVERT: Y 54 ARG cc_start: 0.5145 (ttt180) cc_final: 0.3987 (ttm170) REVERT: N 98 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7974 (mtpp) outliers start: 77 outliers final: 58 residues processed: 558 average time/residue: 1.2642 time to fit residues: 1110.8592 Evaluate side-chains 521 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 461 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 130 CYS Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 161 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 207 ILE Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain r residue 54 HIS Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 329 optimal weight: 10.0000 chunk 266 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 346 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS G 68 ASN H 121 GLN J 47 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 190 ASN r 22 ASN Y 4 HIS N 10 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 56943 Z= 0.335 Angle : 0.775 18.362 84385 Z= 0.408 Chirality : 0.102 1.857 10647 Planarity : 0.006 0.067 5108 Dihedral : 24.263 178.711 26810 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.66 % Favored : 89.26 % Rotamer: Outliers : 4.25 % Allowed : 15.40 % Favored : 80.35 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.66 (0.17), residues: 2524 helix: 0.77 (0.16), residues: 1065 sheet: -2.17 (0.24), residues: 410 loop : -2.69 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 162 HIS 0.007 0.001 HIS S 14 PHE 0.018 0.002 PHE C 129 TYR 0.032 0.002 TYR O 78 ARG 0.006 0.001 ARG D 3 *********************** 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 569 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 478 time to evaluate : 3.778 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: B 24 THR cc_start: 0.9180 (m) cc_final: 0.8732 (p) REVERT: B 29 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7732 (mtp-110) REVERT: F 76 ASP cc_start: 0.8229 (m-30) cc_final: 0.7897 (m-30) REVERT: G 25 GLN cc_start: 0.7711 (tt0) cc_final: 0.7416 (tt0) REVERT: G 106 ASN cc_start: 0.8336 (m-40) cc_final: 0.7919 (t0) REVERT: I 51 ASP cc_start: 0.6626 (m-30) cc_final: 0.5284 (t0) REVERT: I 147 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8117 (t80) REVERT: K 135 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7318 (ttp-110) REVERT: L 70 GLU cc_start: 0.7723 (pm20) cc_final: 0.7510 (pm20) REVERT: P 8 THR cc_start: 0.9128 (t) cc_final: 0.8754 (p) REVERT: S 26 ASN cc_start: 0.8132 (m-40) cc_final: 0.7743 (m-40) REVERT: Y 54 ARG cc_start: 0.5304 (ttt180) cc_final: 0.3957 (ttm170) REVERT: N 98 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8086 (mtpp) outliers start: 91 outliers final: 71 residues processed: 528 average time/residue: 1.2472 time to fit residues: 1040.4426 Evaluate side-chains 525 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 452 time to evaluate : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain K residue 135 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 77 GLN Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 161 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 207 ILE Chi-restraints excluded: chain r residue 22 ASN Chi-restraints excluded: chain r residue 54 HIS Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 100 SER 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: 1.9990 chunk 76 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 386 optimal weight: 1.9990 chunk 320 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 68 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 77 GLN V 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 56943 Z= 0.241 Angle : 0.721 18.365 84385 Z= 0.382 Chirality : 0.100 1.842 10647 Planarity : 0.005 0.059 5108 Dihedral : 24.200 177.655 26810 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.87 % Favored : 91.09 % Rotamer: Outliers : 3.83 % Allowed : 17.03 % Favored : 79.14 % 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: -1.38 (0.17), residues: 2524 helix: 1.02 (0.16), residues: 1065 sheet: -2.00 (0.25), residues: 394 loop : -2.57 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 162 HIS 0.005 0.001 HIS r 54 PHE 0.012 0.001 PHE C 129 TYR 0.020 0.001 TYR O 78 ARG 0.004 0.000 ARG C 130 *********************** 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 563 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 481 time to evaluate : 3.737 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: B 24 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 29 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7746 (mtp-110) REVERT: C 183 ASP cc_start: 0.7520 (t0) cc_final: 0.7300 (t0) REVERT: F 1 MET cc_start: 0.5018 (mtm) cc_final: 0.4441 (mtm) REVERT: G 25 GLN cc_start: 0.7657 (tt0) cc_final: 0.7449 (tt0) REVERT: G 106 ASN cc_start: 0.8311 (m-40) cc_final: 0.7925 (t0) REVERT: H 115 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7561 (t0) REVERT: I 51 ASP cc_start: 0.6558 (m-30) cc_final: 0.5156 (t0) REVERT: I 147 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7842 (t80) REVERT: K 135 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7247 (ttp-110) REVERT: M 116 THR cc_start: 0.7322 (m) cc_final: 0.7057 (t) REVERT: P 8 THR cc_start: 0.9121 (t) cc_final: 0.8738 (p) REVERT: S 26 ASN cc_start: 0.8084 (m-40) cc_final: 0.7726 (m-40) REVERT: V 89 MET cc_start: 0.2771 (mmp) cc_final: 0.2161 (mtt) REVERT: Y 61 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8155 (mt-10) REVERT: N 86 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8145 (tm-30) REVERT: N 98 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8088 (mtpp) outliers start: 82 outliers final: 63 residues processed: 526 average time/residue: 1.2467 time to fit residues: 1036.3388 Evaluate side-chains 525 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 458 time to evaluate : 3.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 135 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 161 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 207 ILE Chi-restraints excluded: chain r residue 22 ASN Chi-restraints excluded: chain r residue 54 HIS Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain g residue 78 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 281 optimal weight: 0.4980 chunk 218 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 384 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 68 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 56943 Z= 0.193 Angle : 0.690 18.336 84385 Z= 0.368 Chirality : 0.100 1.777 10647 Planarity : 0.005 0.059 5108 Dihedral : 24.117 178.746 26810 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.87 % Favored : 91.09 % Rotamer: Outliers : 3.22 % Allowed : 17.97 % Favored : 78.81 % 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: -1.10 (0.17), residues: 2524 helix: 1.29 (0.16), residues: 1065 sheet: -1.90 (0.25), residues: 397 loop : -2.43 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 165 HIS 0.004 0.001 HIS r 54 PHE 0.017 0.001 PHE Y 41 TYR 0.023 0.001 TYR O 78 ARG 0.007 0.000 ARG V 152 *********************** 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 553 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 484 time to evaluate : 3.759 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: B 24 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8661 (p) REVERT: B 29 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7789 (mtp-110) REVERT: C 183 ASP cc_start: 0.7536 (t0) cc_final: 0.7288 (t0) REVERT: G 25 GLN cc_start: 0.7670 (tt0) cc_final: 0.7468 (tt0) REVERT: G 106 ASN cc_start: 0.8271 (m-40) cc_final: 0.7917 (t0) REVERT: H 115 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7617 (t0) REVERT: I 51 ASP cc_start: 0.6647 (m-30) cc_final: 0.5195 (t0) REVERT: I 147 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7965 (t80) REVERT: K 135 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7219 (ttp-110) REVERT: M 116 THR cc_start: 0.7379 (m) cc_final: 0.7164 (t) REVERT: P 8 THR cc_start: 0.9081 (t) cc_final: 0.8482 (p) REVERT: S 26 ASN cc_start: 0.8021 (m-40) cc_final: 0.7664 (m-40) REVERT: Y 65 ARG cc_start: 0.6796 (mtm180) cc_final: 0.5715 (mtp85) REVERT: Y 74 GLU cc_start: 0.7251 (tt0) cc_final: 0.6902 (tt0) REVERT: N 98 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8061 (mtpp) outliers start: 69 outliers final: 57 residues processed: 520 average time/residue: 1.2069 time to fit residues: 989.9496 Evaluate side-chains 517 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 456 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 135 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain V residue 38 ILE Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 161 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 192 ASP Chi-restraints excluded: chain V residue 207 ILE Chi-restraints excluded: chain r residue 54 HIS Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 237 optimal weight: 2.9990 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: 0.0980 chunk 262 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 167 GLN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 56943 Z= 0.310 Angle : 0.752 18.389 84385 Z= 0.397 Chirality : 0.102 1.912 10647 Planarity : 0.005 0.060 5108 Dihedral : 24.223 177.332 26810 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.18 % Favored : 89.78 % Rotamer: Outliers : 3.64 % Allowed : 17.92 % Favored : 78.44 % 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: -1.27 (0.17), residues: 2524 helix: 1.07 (0.16), residues: 1065 sheet: -1.93 (0.25), residues: 401 loop : -2.44 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 165 HIS 0.006 0.001 HIS K 127 PHE 0.013 0.002 PHE D 67 TYR 0.021 0.002 TYR O 78 ARG 0.006 0.001 ARG K 102 *********************** 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 548 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 470 time to evaluate : 3.868 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: B 24 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8713 (p) REVERT: B 29 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7883 (mtp-110) REVERT: C 141 MET cc_start: 0.8824 (tpp) cc_final: 0.8575 (tpt) REVERT: G 25 GLN cc_start: 0.7683 (tt0) cc_final: 0.7466 (tt0) REVERT: G 106 ASN cc_start: 0.8330 (m-40) cc_final: 0.7983 (t0) REVERT: H 115 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7647 (t0) REVERT: I 51 ASP cc_start: 0.6752 (m-30) cc_final: 0.5459 (t70) REVERT: I 84 TYR cc_start: 0.7228 (m-80) cc_final: 0.6982 (m-10) REVERT: K 135 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7197 (ttp-110) REVERT: M 116 THR cc_start: 0.7362 (m) cc_final: 0.7146 (t) REVERT: S 26 ASN cc_start: 0.7960 (m-40) cc_final: 0.7492 (m-40) REVERT: Y 21 ARG cc_start: 0.5975 (tpt90) cc_final: 0.5569 (tpm170) REVERT: N 98 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8066 (mtpp) outliers start: 78 outliers final: 71 residues processed: 511 average time/residue: 1.2116 time to fit residues: 970.1724 Evaluate side-chains 535 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 461 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain K residue 135 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 79 MET Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 56 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 38 ILE Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 161 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 192 ASP Chi-restraints excluded: chain V residue 207 ILE Chi-restraints excluded: chain r residue 54 HIS Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain g residue 78 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 349 optimal weight: 9.9990 chunk 368 optimal weight: 0.0040 chunk 336 optimal weight: 4.9990 chunk 358 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 281 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 323 optimal weight: 0.0070 chunk 338 optimal weight: 4.9990 chunk 357 optimal weight: 7.9990 overall best weight: 2.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN ** O 28 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 56943 Z= 0.268 Angle : 0.726 18.316 84385 Z= 0.385 Chirality : 0.101 1.816 10647 Planarity : 0.005 0.060 5108 Dihedral : 24.183 177.680 26810 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.59 % Favored : 90.37 % Rotamer: Outliers : 3.59 % Allowed : 18.53 % Favored : 77.88 % 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: -1.18 (0.17), residues: 2524 helix: 1.12 (0.16), residues: 1065 sheet: -1.94 (0.25), residues: 407 loop : -2.35 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 165 HIS 0.005 0.001 HIS r 54 PHE 0.012 0.002 PHE Y 34 TYR 0.023 0.001 TYR O 78 ARG 0.006 0.000 ARG L 13 *********************** 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 553 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 476 time to evaluate : 3.922 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: B 24 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8699 (p) REVERT: B 29 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7888 (mtp-110) REVERT: C 141 MET cc_start: 0.8802 (tpp) cc_final: 0.8541 (tpt) REVERT: G 25 GLN cc_start: 0.7714 (tt0) cc_final: 0.7513 (tt0) REVERT: G 106 ASN cc_start: 0.8344 (m-40) cc_final: 0.8017 (t0) REVERT: H 115 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7669 (t0) REVERT: I 51 ASP cc_start: 0.6697 (m-30) cc_final: 0.5424 (t70) REVERT: I 84 TYR cc_start: 0.7237 (m-80) cc_final: 0.7000 (m-10) REVERT: K 135 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7183 (ttp-110) REVERT: M 67 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6663 (mm-30) REVERT: S 26 ASN cc_start: 0.8053 (m-40) cc_final: 0.7640 (m-40) REVERT: Y 62 ILE cc_start: 0.8505 (mt) cc_final: 0.8205 (pt) REVERT: N 98 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8053 (mtpp) outliers start: 77 outliers final: 67 residues processed: 520 average time/residue: 1.2329 time to fit residues: 1004.0372 Evaluate side-chains 532 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 462 time to evaluate : 3.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 135 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 56 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 161 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 192 ASP Chi-restraints excluded: chain V residue 207 ILE Chi-restraints excluded: chain r residue 54 HIS Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain g residue 78 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 235 optimal weight: 5.9990 chunk 378 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 263 optimal weight: 0.5980 chunk 397 optimal weight: 0.1980 chunk 365 optimal weight: 5.9990 chunk 316 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 28 GLN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 56943 Z= 0.144 Angle : 0.674 18.293 84385 Z= 0.360 Chirality : 0.099 1.745 10647 Planarity : 0.004 0.059 5108 Dihedral : 24.057 179.541 26810 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.55 % Rotamer: Outliers : 2.01 % Allowed : 20.25 % Favored : 77.74 % 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: -0.75 (0.17), residues: 2524 helix: 1.47 (0.16), residues: 1070 sheet: -1.65 (0.25), residues: 410 loop : -2.17 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 103 HIS 0.003 0.001 HIS E 108 PHE 0.010 0.001 PHE Y 41 TYR 0.025 0.001 TYR O 78 ARG 0.006 0.000 ARG K 102 ********************** 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 530 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 487 time to evaluate : 3.826 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: B 24 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8597 (p) REVERT: B 29 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7824 (mtp-110) REVERT: C 141 MET cc_start: 0.8794 (tpp) cc_final: 0.8559 (tpt) REVERT: G 106 ASN cc_start: 0.8232 (m-40) cc_final: 0.7963 (t0) REVERT: I 51 ASP cc_start: 0.6577 (m-30) cc_final: 0.4990 (t0) REVERT: I 84 TYR cc_start: 0.7052 (m-80) cc_final: 0.6800 (m-10) REVERT: K 45 ASP cc_start: 0.7309 (m-30) cc_final: 0.7088 (m-30) REVERT: K 65 ARG cc_start: 0.8397 (mtp180) cc_final: 0.8053 (mtt180) REVERT: M 65 LYS cc_start: 0.6876 (ptpp) cc_final: 0.6527 (ptpp) REVERT: M 67 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6651 (mm-30) REVERT: O 82 ILE cc_start: 0.9016 (mt) cc_final: 0.8707 (mt) REVERT: Q 60 LYS cc_start: 0.8056 (mttt) cc_final: 0.7689 (mttm) REVERT: S 26 ASN cc_start: 0.8002 (m-40) cc_final: 0.7602 (m-40) REVERT: Y 21 ARG cc_start: 0.6006 (tpt90) cc_final: 0.5533 (tpm170) REVERT: Y 80 PHE cc_start: 0.6569 (p90) cc_final: 0.5854 (p90) REVERT: N 98 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8016 (mtpp) outliers start: 43 outliers final: 38 residues processed: 510 average time/residue: 1.2442 time to fit residues: 1000.4934 Evaluate side-chains 504 residues out of total 2143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 465 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain Q residue 56 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 161 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 192 ASP Chi-restraints excluded: chain V residue 207 ILE Chi-restraints excluded: chain r residue 54 HIS Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain g residue 78 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 251 optimal weight: 0.8980 chunk 337 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 317 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 28 GLN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.101360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084466 restraints weight = 385046.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086567 restraints weight = 138758.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087808 restraints weight = 82515.315| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 56943 Z= 0.246 Angle : 0.706 18.356 84385 Z= 0.375 Chirality : 0.100 1.847 10647 Planarity : 0.005 0.061 5108 Dihedral : 24.093 177.765 26810 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.07 % Favored : 90.89 % Rotamer: Outliers : 2.24 % Allowed : 20.49 % Favored : 77.27 % 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: -0.82 (0.17), residues: 2524 helix: 1.41 (0.16), residues: 1067 sheet: -1.63 (0.26), residues: 402 loop : -2.20 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 103 HIS 0.004 0.001 HIS K 127 PHE 0.013 0.001 PHE V 16 TYR 0.021 0.001 TYR O 78 ARG 0.006 0.000 ARG K 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25377.49 seconds wall clock time: 440 minutes 10.25 seconds (26410.25 seconds total)