Starting phenix.real_space_refine (version: dev) on Sun Apr 10 00:17:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/04_2022/5o5j_3748.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/04_2022/5o5j_3748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/04_2022/5o5j_3748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/04_2022/5o5j_3748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/04_2022/5o5j_3748.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/04_2022/5o5j_3748.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D GLU 73": "OE1" <-> "OE2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "V GLU 169": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 52163 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 32439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1511, 32439 Classifications: {'RNA': 1511} Modifications used: {'rna3p_pyr': 577, 'rna2p_pur': 112, 'rna3p_pur': 737, 'rna2p_pyr': 85} Link IDs: {'rna3p': 1313, 'rna2p': 197} Chain: "B" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 280 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1660 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "E" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1296 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain: "F" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "G" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "H" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "I" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "J" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "K" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 855 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "M" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "N" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "O" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "P" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "Q" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 513 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "S" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 662 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "V" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "W" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 410 Classifications: {'RNA': 19} Modifications used: {'rna3p_pyr': 7, 'rna3p_pur': 12} Link IDs: {'rna3p': 18} Chain: "X" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'rna3p_pyr': 6, '5*END': 1} Link IDs: {'rna3p': 5} Chain: "g" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 215 Unusual residues: {' MG': 215} Classifications: {'undetermined': 215} Link IDs: {None: 214} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 45043 SG CYS N 24 57.685 122.311 115.050 1.00 34.82 S ATOM 45066 SG CYS N 27 61.429 120.802 115.181 1.00 47.23 S ATOM 45172 SG CYS N 40 60.843 122.916 112.320 1.00 52.70 S ATOM 45197 SG CYS N 43 59.422 119.634 112.537 1.00 50.43 S ATOM 47728 SG CYS R 20 115.128 98.193 30.398 1.00 69.69 S ATOM 47752 SG CYS R 23 116.081 94.621 30.826 1.00 84.90 S ATOM 48024 SG CYS R 57 117.174 96.819 33.816 1.00 52.35 S Time building chain proxies: 28.20, per 1000 atoms: 0.54 Number of scatterers: 52163 At special positions: 0 Unit cell: (216.84, 207.11, 189.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 45 16.00 P 1535 15.00 Mg 217 11.99 O 14102 8.00 N 9697 7.00 C 26565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.46 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb=" ZN R 102 " pdb="ZN ZN R 102 " - pdb=" ND1 HIS R 60 " pdb="ZN ZN R 102 " - pdb=" SG CYS R 23 " pdb="ZN ZN R 102 " - pdb=" SG CYS R 57 " pdb="ZN ZN R 102 " - pdb=" SG CYS R 20 " Number of angles added : 9 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 20 sheets defined 45.9% alpha, 16.6% beta 502 base pairs and 824 stacking pairs defined. Time for finding SS restraints: 20.79 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 removed outlier: 4.685A pdb=" N LYS B 7 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 33 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 27 through 46 removed outlier: 3.914A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.605A pdb=" N ILE C 74 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 128 through 143 removed outlier: 3.889A pdb=" N GLN C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.329A pdb=" N LYS D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 12 " --> pdb=" O ALA D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 29 removed outlier: 3.791A pdb=" N GLU D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 removed outlier: 3.873A pdb=" N LEU D 50 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 77 Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.770A pdb=" N ASN D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 182 through 187 removed outlier: 3.683A pdb=" N ASP D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 201 removed outlier: 3.599A pdb=" N TYR D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 95 Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.621A pdb=" N LEU E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 185 through 190 removed outlier: 3.815A pdb=" N VAL E 189 " --> pdb=" O PRO E 185 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 190' Processing helix chain 'E' and resid 191 through 214 removed outlier: 3.506A pdb=" N ALA E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 18 through 34 removed outlier: 3.844A pdb=" N VAL F 29 " --> pdb=" O THR F 25 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE F 30 " --> pdb=" O PHE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 3.531A pdb=" N SER F 73 " --> pdb=" O PRO F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.847A pdb=" N THR G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.575A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 Processing helix chain 'G' and resid 92 through 109 removed outlier: 3.578A pdb=" N SER G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.720A pdb=" N ALA G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 148 removed outlier: 3.945A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 155 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 115 through 121 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 removed outlier: 3.687A pdb=" N ILE I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 119 Processing helix chain 'J' and resid 14 through 32 removed outlier: 3.734A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.628A 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 62 through 67 removed outlier: 3.748A pdb=" N ARG K 65 " --> pdb=" O LYS K 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER K 67 " --> pdb=" O SER K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 85 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'L' and resid 3 through 11 Processing helix chain 'L' and resid 21 through 25 removed outlier: 3.709A pdb=" N LEU L 24 " --> pdb=" O THR L 21 " (cutoff:3.500A) 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 removed outlier: 3.883A pdb=" N ALA M 35 " --> pdb=" O ASN M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 64 Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.762A pdb=" N LEU M 70 " --> pdb=" O VAL M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 3 through 11 removed outlier: 3.539A pdb=" N ASN N 11 " --> pdb=" O VAL N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 20 removed outlier: 3.623A pdb=" N ALA N 20 " --> pdb=" O ALA N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.663A pdb=" N VAL O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.557A pdb=" N ARG O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 3.826A 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 'R' and resid 34 through 41 removed outlier: 3.903A pdb=" N LEU R 38 " --> pdb=" O ASP R 34 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 57 through 74 Processing helix chain 'S' and resid 4 through 8 removed outlier: 3.520A pdb=" N LYS S 7 " --> pdb=" O SER S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 70 through 75 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.560A pdb=" N ILE T 8 " --> pdb=" O ILE T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 63 removed outlier: 3.522A 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 Processing helix chain 'V' and resid 24 through 28 Processing helix chain 'V' and resid 42 through 63 Processing helix chain 'V' and resid 73 through 88 removed outlier: 4.680A pdb=" N GLU V 78 " --> pdb=" O LYS V 74 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER V 79 " --> pdb=" O GLN V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 108 removed outlier: 4.041A pdb=" N VAL V 107 " --> pdb=" O ASN V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 123 removed outlier: 3.590A pdb=" N THR V 123 " --> pdb=" O ALA V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 148 removed outlier: 3.772A pdb=" N LEU V 135 " --> pdb=" O LYS V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 155 removed outlier: 3.537A pdb=" N ASP V 153 " --> pdb=" O GLY V 149 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN V 155 " --> pdb=" O ILE V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 169 through 179 removed outlier: 3.738A pdb=" N VAL V 173 " --> pdb=" O GLU V 169 " (cutoff:3.500A) Processing helix chain 'V' and resid 192 through 196 removed outlier: 3.618A pdb=" N VAL V 195 " --> pdb=" O ASP V 192 " (cutoff:3.500A) removed outlier: 3.748A 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 'g' and resid 57 through 65 removed outlier: 3.650A pdb=" N ARG g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 98 through 104 removed outlier: 6.781A pdb=" N VAL C 63 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN C 101 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 67 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 164 through 170 removed outlier: 6.800A pdb=" N TYR C 203 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE C 149 " --> pdb=" O TRP C 201 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP C 201 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL C 151 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS C 199 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS C 153 " --> pdb=" O GLY C 197 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY C 197 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLY C 155 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ARG C 195 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 118 through 120 Processing sheet with id= D, first strand: chain 'E' and resid 71 through 78 removed outlier: 3.830A pdb=" N SER E 42 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 63 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL E 40 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY E 65 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU E 38 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 110 through 114 removed outlier: 3.726A pdb=" N VAL E 118 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 154 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET E 120 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER E 152 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG E 122 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA E 150 " --> pdb=" O ARG E 122 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 37 through 43 removed outlier: 6.741A pdb=" N ASP F 11 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL F 85 " --> pdb=" O ASP F 11 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 73 through 80 Processing sheet with id= H, first strand: chain 'H' and resid 24 through 28 Processing sheet with id= I, first strand: chain 'H' and resid 76 through 79 removed outlier: 6.607A pdb=" N ILE H 105 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR H 130 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL H 103 " --> pdb=" O TYR H 130 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 28 through 31 Processing sheet with id= K, first strand: chain 'J' and resid 70 through 77 Processing sheet with id= L, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= M, first strand: chain 'K' and resid 50 through 55 removed outlier: 6.845A pdb=" N ILE K 43 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP K 53 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL K 41 " --> pdb=" O TRP K 53 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER K 55 " --> pdb=" O THR K 39 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR K 39 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN K 38 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS K 90 " --> pdb=" O GLY K 28 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA K 30 " --> pdb=" O LYS K 90 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP K 92 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE K 32 " --> pdb=" O ASP K 92 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE K 94 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER K 34 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS K 96 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLU K 115 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL K 93 " --> pdb=" O GLU K 115 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY K 117 " --> pdb=" O VAL K 93 " (cutoff:3.500A) removed outlier: 11.573A pdb=" N VAL K 95 " --> pdb=" O GLY K 117 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ILE K 119 " --> pdb=" O VAL K 95 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 29 through 33 removed outlier: 4.063A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LYS L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N CYS L 34 " --> pdb=" O LYS L 56 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'P' and resid 3 through 10 removed outlier: 6.704A pdb=" N VAL P 22 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL P 36 " --> pdb=" O VAL P 22 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Q' and resid 22 through 26 removed outlier: 8.899A pdb=" N ARG Q 87 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LYS Q 60 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG Q 89 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS Q 62 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER Q 29 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU Q 39 " --> pdb=" O VAL Q 27 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL Q 27 " --> pdb=" O GLU Q 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'Q' and resid 73 through 75 removed outlier: 6.442A pdb=" N SER Q 75 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE Q 93 " --> pdb=" O SER Q 75 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'S' and resid 30 through 33 removed outlier: 7.229A pdb=" N THR S 48 " --> pdb=" O ILE S 31 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR S 33 " --> pdb=" O THR S 48 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA S 50 " --> pdb=" O THR S 33 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'V' and resid 67 through 70 removed outlier: 7.328A pdb=" N ALA V 160 " --> pdb=" O LEU V 68 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL V 70 " --> pdb=" O ALA V 160 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP V 162 " --> pdb=" O VAL V 70 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL V 163 " --> pdb=" O PRO V 182 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE V 184 " --> pdb=" O VAL V 163 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR V 198 " --> pdb=" O ALA V 185 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU V 187 " --> pdb=" O TYR V 198 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE V 200 " --> pdb=" O LEU V 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'V' and resid 31 through 34 removed outlier: 6.681A pdb=" N ILE V 40 " --> pdb=" O PHE V 32 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1271 hydrogen bonds 1996 hydrogen bond angles 0 basepair planarities 502 basepair parallelities 824 stacking parallelities Total time for adding SS restraints: 49.91 Time building geometry restraints manager: 25.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6033 1.32 - 1.45: 24329 1.45 - 1.58: 22683 1.58 - 1.71: 3042 1.71 - 1.84: 76 Bond restraints: 56163 Sorted by residual: bond pdb=" CA VAL V 157 " pdb=" CB VAL V 157 " ideal model delta sigma weight residual 1.537 1.602 -0.065 1.29e-02 6.01e+03 2.51e+01 bond pdb=" CA VAL R 58 " pdb=" CB VAL R 58 " ideal model delta sigma weight residual 1.539 1.491 0.048 1.11e-02 8.12e+03 1.83e+01 bond pdb=" CA ILE E 63 " pdb=" CB ILE E 63 " ideal model delta sigma weight residual 1.540 1.489 0.052 1.23e-02 6.61e+03 1.76e+01 bond pdb=" CA VAL H 123 " pdb=" CB VAL H 123 " ideal model delta sigma weight residual 1.540 1.484 0.056 1.36e-02 5.41e+03 1.68e+01 bond pdb=" CA ILE C 202 " pdb=" CB ILE C 202 " ideal model delta sigma weight residual 1.537 1.491 0.046 1.26e-02 6.30e+03 1.35e+01 ... (remaining 56158 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.40: 9637 106.40 - 113.78: 33549 113.78 - 121.15: 24579 121.15 - 128.53: 13557 128.53 - 135.90: 2143 Bond angle restraints: 83465 Sorted by residual: angle pdb=" C GLY K 97 " pdb=" N PRO K 98 " pdb=" CA PRO K 98 " ideal model delta sigma weight residual 119.89 128.98 -9.09 1.02e+00 9.61e-01 7.95e+01 angle pdb=" C LYS J 57 " pdb=" CA LYS J 57 " pdb=" CB LYS J 57 " ideal model delta sigma weight residual 115.89 104.29 11.60 1.32e+00 5.74e-01 7.72e+01 angle pdb=" C PRO D 32 " pdb=" N PRO D 33 " pdb=" CA PRO D 33 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.55e+01 angle pdb=" C3' U A1482 " pdb=" O3' U A1482 " pdb=" P A A1483 " ideal model delta sigma weight residual 120.20 131.16 -10.96 1.50e+00 4.44e-01 5.34e+01 angle pdb=" C VAL E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta sigma weight residual 119.84 128.95 -9.11 1.25e+00 6.40e-01 5.31e+01 ... (remaining 83460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 28732 35.62 - 71.24: 1519 71.24 - 106.85: 103 106.85 - 142.47: 17 142.47 - 178.09: 20 Dihedral angle restraints: 30391 sinusoidal: 23506 harmonic: 6885 Sorted by residual: dihedral pdb=" O4' U A 328 " pdb=" C1' U A 328 " pdb=" N1 U A 328 " pdb=" C2 U A 328 " ideal model delta sinusoidal sigma weight residual -160.00 18.09 -178.09 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 415 " pdb=" C1' C A 415 " pdb=" N1 C A 415 " pdb=" C2 C A 415 " ideal model delta sinusoidal sigma weight residual -160.00 15.14 -175.14 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A 179 " pdb=" C1' C A 179 " pdb=" N1 C A 179 " pdb=" C2 C A 179 " ideal model delta sinusoidal sigma weight residual 200.00 28.03 171.97 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 30388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 10321 0.125 - 0.250: 245 0.250 - 0.374: 7 0.374 - 0.499: 2 0.499 - 0.624: 1 Chirality restraints: 10576 Sorted by residual: chirality pdb=" C3' U A1482 " pdb=" C4' U A1482 " pdb=" O3' U A1482 " pdb=" C2' U A1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" C3' A A 895 " pdb=" C4' A A 895 " pdb=" O3' A A 895 " pdb=" C2' A A 895 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C1' G A 713 " pdb=" O4' G A 713 " pdb=" C2' G A 713 " pdb=" N9 G A 713 " both_signs ideal model delta sigma weight residual False 2.46 2.05 0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 10573 not shown) Planarity restraints: 4881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 953 " -0.048 2.00e-02 2.50e+03 2.41e-02 1.74e+01 pdb=" N9 G A 953 " 0.066 2.00e-02 2.50e+03 pdb=" C8 G A 953 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G A 953 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 953 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G A 953 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G A 953 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G A 953 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 953 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G A 953 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A 953 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G A 953 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 110 " 0.050 2.00e-02 2.50e+03 2.47e-02 1.37e+01 pdb=" N1 U A 110 " -0.046 2.00e-02 2.50e+03 pdb=" C2 U A 110 " -0.019 2.00e-02 2.50e+03 pdb=" O2 U A 110 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A 110 " -0.005 2.00e-02 2.50e+03 pdb=" C4 U A 110 " 0.009 2.00e-02 2.50e+03 pdb=" O4 U A 110 " 0.018 2.00e-02 2.50e+03 pdb=" C5 U A 110 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A 110 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 67 " -0.039 2.00e-02 2.50e+03 2.24e-02 1.13e+01 pdb=" N1 C A 67 " 0.053 2.00e-02 2.50e+03 pdb=" C2 C A 67 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C A 67 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C A 67 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C A 67 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C A 67 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C A 67 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C A 67 " 0.005 2.00e-02 2.50e+03 ... (remaining 4878 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 153 2.37 - 3.00: 26062 3.00 - 3.64: 87320 3.64 - 4.27: 150925 4.27 - 4.90: 203922 Nonbonded interactions: 468382 Sorted by model distance: nonbonded pdb=" OP2 A A 540 " pdb="MG MG A1615 " model vdw 1.740 2.170 nonbonded pdb=" OP1 G A 455 " pdb="MG MG A1710 " model vdw 1.818 2.170 nonbonded pdb=" OP2 A A 513 " pdb="MG MG A1765 " model vdw 1.824 2.170 nonbonded pdb=" OP1 C A 961 " pdb="MG MG A1669 " model vdw 1.849 2.170 nonbonded pdb=" OP1 U A1205 " pdb="MG MG A1639 " model vdw 1.867 2.170 ... (remaining 468377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1535 5.49 5 Mg 217 5.21 5 S 45 5.16 5 C 26565 2.51 5 N 9697 2.21 5 O 14102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.190 Check model and map are aligned: 0.700 Convert atoms to be neutral: 0.400 Process input model: 177.290 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 0.077 56163 Z= 0.495 Angle : 1.198 13.237 83465 Z= 0.687 Chirality : 0.050 0.624 10576 Planarity : 0.006 0.069 4881 Dihedral : 17.479 178.090 25957 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.46 % Rotamer Outliers : 11.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.13), residues: 2364 helix: -3.17 (0.11), residues: 1012 sheet: -0.76 (0.22), residues: 399 loop : -2.03 (0.16), residues: 953 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 865 time to evaluate : 3.290 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 outliers start: 233 outliers final: 75 residues processed: 1017 average time/residue: 0.7743 time to fit residues: 1209.5114 Evaluate side-chains 661 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 586 time to evaluate : 2.982 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.5362 time to fit residues: 74.1742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 196 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 348 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN C 111 GLN C 138 GLN D 66 GLN D 151 GLN E 157 ASN E 160 ASN F 96 HIS G 28 ASN G 142 HIS H 121 GLN I 57 ASN I 64 HIS I 146 GLN J 70 HIS ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN L 73 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 HIS Q 46 HIS S 14 HIS ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 HIS S 57 HIS T 70 ASN T 74 ASN ** V 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 167 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.092 56163 Z= 0.285 Angle : 0.713 9.759 83465 Z= 0.365 Chirality : 0.041 0.322 10576 Planarity : 0.006 0.085 4881 Dihedral : 16.102 179.490 21129 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.02 % Rotamer Outliers : 5.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2364 helix: -0.34 (0.15), residues: 1013 sheet: -0.14 (0.23), residues: 422 loop : -1.33 (0.19), residues: 929 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 664 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 57 residues processed: 713 average time/residue: 0.6973 time to fit residues: 795.4654 Evaluate side-chains 650 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 593 time to evaluate : 3.604 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.5073 time to fit residues: 56.3217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 349 optimal weight: 20.0000 chunk 377 optimal weight: 8.9990 chunk 311 optimal weight: 6.9990 chunk 346 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS C 138 GLN D 151 GLN G 129 ASN G 142 HIS I 146 GLN J 56 HIS ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 GLN ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN P 57 GLN R 28 GLN ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 56163 Z= 0.245 Angle : 0.640 10.582 83465 Z= 0.329 Chirality : 0.038 0.282 10576 Planarity : 0.005 0.091 4881 Dihedral : 15.681 178.788 21129 Min Nonbonded Distance : 1.003 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Rotamer Outliers : 4.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2364 helix: 0.72 (0.16), residues: 1019 sheet: 0.02 (0.23), residues: 423 loop : -1.02 (0.20), residues: 922 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 624 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 49 residues processed: 665 average time/residue: 0.6683 time to fit residues: 717.4421 Evaluate side-chains 627 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 578 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.4659 time to fit residues: 46.2088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 6.9990 chunk 262 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 350 optimal weight: 30.0000 chunk 371 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 100 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN C 138 GLN D 49 GLN D 51 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS H 35 ASN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN M 42 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 56163 Z= 0.310 Angle : 0.675 12.603 83465 Z= 0.344 Chirality : 0.039 0.297 10576 Planarity : 0.006 0.099 4881 Dihedral : 15.614 179.484 21129 Min Nonbonded Distance : 0.972 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2364 helix: 0.85 (0.16), residues: 1022 sheet: 0.05 (0.24), residues: 429 loop : -0.95 (0.20), residues: 913 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 587 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 50 residues processed: 619 average time/residue: 0.6401 time to fit residues: 634.9065 Evaluate side-chains 614 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 564 time to evaluate : 2.520 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4374 time to fit residues: 44.5260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 189 optimal weight: 30.0000 chunk 333 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN D 49 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN M 42 ASN N 11 ASN P 57 GLN ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 56163 Z= 0.246 Angle : 0.625 13.064 83465 Z= 0.319 Chirality : 0.037 0.275 10576 Planarity : 0.005 0.103 4881 Dihedral : 15.458 179.553 21129 Min Nonbonded Distance : 1.007 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.07 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2364 helix: 1.00 (0.16), residues: 1015 sheet: 0.09 (0.24), residues: 418 loop : -0.90 (0.20), residues: 931 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 578 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 34 residues processed: 601 average time/residue: 0.6367 time to fit residues: 614.4480 Evaluate side-chains 595 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 561 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4139 time to fit residues: 29.3889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 20.0000 chunk 334 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 371 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 195 optimal weight: 6.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.099 56163 Z= 0.277 Angle : 0.651 15.638 83465 Z= 0.332 Chirality : 0.038 0.290 10576 Planarity : 0.005 0.103 4881 Dihedral : 15.448 179.874 21129 Min Nonbonded Distance : 0.993 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.10 % Favored : 95.77 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2364 helix: 1.04 (0.16), residues: 1008 sheet: 0.11 (0.24), residues: 411 loop : -0.89 (0.20), residues: 945 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 565 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 44 residues processed: 589 average time/residue: 0.6091 time to fit residues: 574.9095 Evaluate side-chains 590 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 546 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.4126 time to fit residues: 36.8948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 6.9990 chunk 41 optimal weight: 30.0000 chunk 211 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 312 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 370 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS J 101 GLN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 ASN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.131 56163 Z= 0.277 Angle : 0.651 20.076 83465 Z= 0.334 Chirality : 0.037 0.284 10576 Planarity : 0.005 0.103 4881 Dihedral : 15.431 179.879 21129 Min Nonbonded Distance : 0.992 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.52 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2364 helix: 1.06 (0.16), residues: 1008 sheet: 0.09 (0.25), residues: 409 loop : -0.91 (0.20), residues: 947 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 571 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 30 residues processed: 588 average time/residue: 0.5811 time to fit residues: 546.0894 Evaluate side-chains 581 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 551 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3795 time to fit residues: 24.8306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 221 optimal weight: 0.1980 chunk 111 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 252 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 290 optimal weight: 0.7980 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN M 42 ASN M 63 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 ASN ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.353 56163 Z= 0.244 Angle : 0.639 30.631 83465 Z= 0.332 Chirality : 0.036 0.272 10576 Planarity : 0.005 0.109 4881 Dihedral : 15.349 179.405 21129 Min Nonbonded Distance : 1.009 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.73 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2364 helix: 1.18 (0.16), residues: 1006 sheet: 0.18 (0.25), residues: 414 loop : -0.88 (0.20), residues: 944 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 574 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 585 average time/residue: 0.5550 time to fit residues: 521.0418 Evaluate side-chains 572 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 553 time to evaluate : 2.510 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4036 time to fit residues: 16.7385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 5.9990 chunk 354 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 270 optimal weight: 30.0000 chunk 105 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 326 optimal weight: 0.7980 chunk 343 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 ASN N 11 ASN P 65 GLN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.583 56163 Z= 0.263 Angle : 0.688 73.892 83465 Z= 0.341 Chirality : 0.036 0.315 10576 Planarity : 0.006 0.139 4881 Dihedral : 15.348 179.404 21129 Min Nonbonded Distance : 1.011 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.73 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2364 helix: 1.20 (0.16), residues: 1006 sheet: 0.17 (0.25), residues: 414 loop : -0.87 (0.20), residues: 944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 560 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 566 average time/residue: 0.5563 time to fit residues: 508.0533 Evaluate side-chains 571 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 557 time to evaluate : 2.409 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3744 time to fit residues: 12.4419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 7.9990 chunk 364 optimal weight: 9.9990 chunk 222 optimal weight: 0.0570 chunk 173 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 chunk 382 optimal weight: 30.0000 chunk 352 optimal weight: 10.0000 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 235 optimal weight: 30.0000 chunk 186 optimal weight: 0.6980 overall best weight: 4.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.667 56163 Z= 0.588 Angle : 0.739 73.900 83465 Z= 0.383 Chirality : 0.036 0.315 10576 Planarity : 0.006 0.154 4881 Dihedral : 15.348 179.404 21129 Min Nonbonded Distance : 1.011 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2364 helix: 1.20 (0.16), residues: 1006 sheet: 0.17 (0.25), residues: 414 loop : -0.87 (0.20), residues: 944 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.5746 time to fit residues: 507.2203 Evaluate side-chains 557 residues out of total 2000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 2.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 20.0000 chunk 324 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 280 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 313 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 7.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084718 restraints weight = 129100.345| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 0.96 r_work: 0.3208 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 1.13 restraints_weight: 0.2500 r_work: 0.3178 rms_B_bonded: 1.38 restraints_weight: 0.1250 r_work: 0.3158 rms_B_bonded: 1.73 restraints_weight: 0.0625 r_work: 0.3132 rms_B_bonded: 2.22 restraints_weight: 0.0312 r_work: 0.3096 rms_B_bonded: 2.96 restraints_weight: 0.0156 r_work: 0.3042 rms_B_bonded: 4.14 restraints_weight: 0.0078 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.667 56163 Z= 0.588 Angle : 0.739 73.900 83465 Z= 0.383 Chirality : 0.036 0.315 10576 Planarity : 0.006 0.154 4881 Dihedral : 15.348 179.404 21129 Min Nonbonded Distance : 1.011 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2364 helix: 1.20 (0.16), residues: 1006 sheet: 0.17 (0.25), residues: 414 loop : -0.87 (0.20), residues: 944 =============================================================================== Job complete usr+sys time: 9989.52 seconds wall clock time: 179 minutes 55.97 seconds (10795.97 seconds total)