Starting phenix.real_space_refine on Mon Mar 25 16:26:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/03_2024/6zok_11321.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/03_2024/6zok_11321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/03_2024/6zok_11321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/03_2024/6zok_11321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/03_2024/6zok_11321.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/03_2024/6zok_11321.pdb" } resolution = 2.8 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= -0.002 sd= 0.143 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1232 5.49 5 Mg 109 5.21 5 S 106 5.16 5 C 26776 2.51 5 N 9246 2.21 5 O 12722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 208": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 194": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 150": "NH1" <-> "NH2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L GLU 130": "OE1" <-> "OE2" Residue "N TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "N TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 46": "OD1" <-> "OD2" Residue "R ASP 110": "OD1" <-> "OD2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X GLU 139": "OE1" <-> "OE2" Residue "Y PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 109": "OE1" <-> "OE2" Residue "b GLU 14": "OE1" <-> "OE2" Residue "b ARG 17": "NH1" <-> "NH2" Residue "b PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 148": "OE1" <-> "OE2" Residue "j GLU 172": "OE1" <-> "OE2" Residue "h ARG 6": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50192 Number of models: 1 Model: "" Number of chains: 26 Chain: "2" Number of atoms: 26317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1232, 26317 Classifications: {'RNA': 1232} Modifications used: {'rna2p_pur': 97, 'rna2p_pyr': 71, 'rna3p_pur': 564, 'rna3p_pyr': 500} Link IDs: {'rna2p': 168, 'rna3p': 1063} Chain breaks: 6 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1010 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "R" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 397 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "V" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "e" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 441 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "j" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 267 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "h" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "2" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Unusual residues: {' MG': 106} Classifications: {'undetermined': 106} Link IDs: {None: 105} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 47859 SG CYS a 23 117.904 51.954 131.049 1.00 7.83 S ATOM 47880 SG CYS a 26 114.787 50.718 129.391 1.00 8.94 S ATOM 48263 SG CYS a 74 114.688 53.990 131.361 1.00 8.19 S ATOM 48282 SG CYS a 77 114.887 50.761 133.067 1.00 8.63 S Time building chain proxies: 26.52, per 1000 atoms: 0.53 Number of scatterers: 50192 At special positions: 0 Unit cell: (181.44, 189, 201.96, 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 1 29.99 S 106 16.00 P 1232 15.00 Mg 109 11.99 O 12722 8.00 N 9246 7.00 C 26776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 40 " - pdb=" SG CYS b 59 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.49 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " Number of angles added : 6 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 32 sheets defined 36.2% alpha, 20.0% beta 340 base pairs and 645 stacking pairs defined. Time for finding SS restraints: 20.14 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.688A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.840A pdb=" N SER A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.543A pdb=" N TYR A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.564A pdb=" N ILE A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.655A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 77 through 84 removed outlier: 4.027A pdb=" N ILE C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.561A pdb=" N ASP C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.579A pdb=" N LEU C 102 " --> pdb=" O GLY C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 218 removed outlier: 3.836A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.526A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.505A pdb=" N MET E 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.976A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.567A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 247 through 261 Processing helix chain 'G' and resid 20 through 26 removed outlier: 3.676A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 181 through 230 removed outlier: 3.822A pdb=" N LYS G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 36 through 43 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 87 removed outlier: 3.617A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG H 78 " --> pdb=" O LYS H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.780A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.808A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 130 through 138 Processing helix chain 'I' and resid 142 through 153 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 192 through 206 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 40 through 61 removed outlier: 3.592A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.566A pdb=" N ASN J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.823A pdb=" N MET J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.786A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 171 through 181 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.610A pdb=" N THR L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 53 Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 58 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 removed outlier: 4.084A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'N' and resid 142 through 150 removed outlier: 4.240A pdb=" N SER N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA N 148 " --> pdb=" O SER N 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 66 through 69 removed outlier: 4.294A pdb=" N SER O 69 " --> pdb=" O ARG O 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 66 through 69' Processing helix chain 'O' and resid 70 through 89 Processing helix chain 'O' and resid 111 through 122 Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'V' and resid 56 through 63 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.757A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.745A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 removed outlier: 3.714A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 21 Processing helix chain 'X' and resid 24 through 33 removed outlier: 4.462A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 39 Processing helix chain 'X' and resid 89 through 94 removed outlier: 3.518A pdb=" N ASN X 92 " --> pdb=" O GLY X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 94 removed outlier: 3.592A pdb=" N HIS Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 114 Processing helix chain 'Y' and resid 119 through 125 Processing helix chain 'a' and resid 46 through 57 removed outlier: 3.665A pdb=" N ARG a 51 " --> pdb=" O ALA a 47 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU a 55 " --> pdb=" O ARG a 51 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA a 56 " --> pdb=" O ASP a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 81 Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'e' and resid 30 through 42 Processing helix chain 'j' and resid 152 through 161 Processing helix chain 'j' and resid 165 through 179 removed outlier: 3.506A pdb=" N GLY j 179 " --> pdb=" O ARG j 175 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 21 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 7.012A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.736A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 124 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.238A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.238A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 13.359A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.137A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N PHE B 211 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N PHE B 142 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG B 213 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL B 140 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 219 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 115 removed outlier: 6.609A pdb=" N PHE C 127 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 109 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS C 125 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG C 123 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN C 113 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG C 121 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AA7, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AA8, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AA9, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.576A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.080A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 217 through 221 removed outlier: 3.880A pdb=" N ASN E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.361A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL G 112 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE G 52 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL G 114 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL G 50 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB5, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 53 removed outlier: 6.815A pdb=" N LYS H 58 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 185 through 188 removed outlier: 8.361A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY H 141 " --> pdb=" O HIS H 157 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS H 142 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.346A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.233A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 62 through 67 removed outlier: 6.030A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP I 105 " --> pdb=" O ARG I 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AC3, first strand: chain 'L' and resid 72 through 82 removed outlier: 16.839A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.843A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS L 81 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.823A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AC6, first strand: chain 'V' and resid 32 through 39 removed outlier: 6.633A pdb=" N ILE V 32 " --> pdb=" O TYR V 53 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR V 53 " --> pdb=" O ILE V 32 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET V 34 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS V 51 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL V 36 " --> pdb=" O GLN V 49 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN V 49 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLU V 38 " --> pdb=" O ASN V 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AC8, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.591A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.500A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N PHE X 120 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR X 82 " --> pdb=" O PHE X 120 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL X 122 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE X 84 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N LYS X 124 " --> pdb=" O PHE X 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 6 through 15 removed outlier: 4.289A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AD3, first strand: chain 'a' and resid 36 through 43 Processing sheet with id=AD4, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AD5, first strand: chain 'b' and resid 54 through 55 removed outlier: 6.703A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 858 hydrogen bonds 1388 hydrogen bond angles 0 basepair planarities 340 basepair parallelities 645 stacking parallelities Total time for adding SS restraints: 34.66 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: 1.21 - 1.34: 11480 1.34 - 1.46: 18664 1.46 - 1.58: 20838 1.58 - 1.70: 2457 1.70 - 1.83: 164 Bond restraints: 53603 Sorted by residual: bond pdb=" N GLU G 118 " pdb=" CA GLU G 118 " ideal model delta sigma weight residual 1.459 1.475 -0.017 1.16e-02 7.43e+03 2.11e+00 bond pdb=" N GLY G 117 " pdb=" CA GLY G 117 " ideal model delta sigma weight residual 1.445 1.455 -0.011 9.20e-03 1.18e+04 1.34e+00 bond pdb=" N1 C 21717 " pdb=" C2 C 21717 " ideal model delta sigma weight residual 1.397 1.418 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" CA TYR E 149 " pdb=" CB TYR E 149 " ideal model delta sigma weight residual 1.522 1.530 -0.007 7.00e-03 2.04e+04 1.09e+00 bond pdb=" N PRO A 207 " pdb=" CA PRO A 207 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.44e-01 ... (remaining 53598 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.98: 7793 106.98 - 113.75: 31984 113.75 - 120.53: 20349 120.53 - 127.30: 15430 127.30 - 134.07: 2702 Bond angle restraints: 78258 Sorted by residual: angle pdb=" N GLU X 53 " pdb=" CA GLU X 53 " pdb=" C GLU X 53 " ideal model delta sigma weight residual 107.88 113.44 -5.56 1.41e+00 5.03e-01 1.55e+01 angle pdb=" C PRO H 65 " pdb=" N VAL H 66 " pdb=" CA VAL H 66 " ideal model delta sigma weight residual 120.33 123.11 -2.78 8.00e-01 1.56e+00 1.21e+01 angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C1' C 2 501 " pdb=" N1 C 2 501 " pdb=" C2 C 2 501 " ideal model delta sigma weight residual 118.80 127.98 -9.18 3.00e+00 1.11e-01 9.36e+00 angle pdb=" C2' U 2 918 " pdb=" C1' U 2 918 " pdb=" N1 U 2 918 " ideal model delta sigma weight residual 112.00 116.28 -4.28 1.50e+00 4.44e-01 8.13e+00 ... (remaining 78253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 30985 35.97 - 71.94: 2858 71.94 - 107.91: 359 107.91 - 143.88: 5 143.88 - 179.85: 13 Dihedral angle restraints: 34220 sinusoidal: 25689 harmonic: 8531 Sorted by residual: dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual 200.00 28.65 171.35 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U 2 823 " pdb=" C1' U 2 823 " pdb=" N1 U 2 823 " pdb=" C2 U 2 823 " ideal model delta sinusoidal sigma weight residual -160.00 7.61 -167.61 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual -160.00 -1.87 -158.13 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 34217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 8541 0.049 - 0.097: 918 0.097 - 0.146: 253 0.146 - 0.195: 12 0.195 - 0.244: 4 Chirality restraints: 9728 Sorted by residual: chirality pdb=" C1' U 2 918 " pdb=" O4' U 2 918 " pdb=" C2' U 2 918 " pdb=" N1 U 2 918 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' G 2 470 " pdb=" O4' G 2 470 " pdb=" C2' G 2 470 " pdb=" N9 G 2 470 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1' G 2 659 " pdb=" O4' G 2 659 " pdb=" C2' G 2 659 " pdb=" N9 G 2 659 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 9725 not shown) Planarity restraints: 5356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 2 60 " 0.032 2.00e-02 2.50e+03 1.44e-02 5.67e+00 pdb=" N9 A 2 60 " -0.033 2.00e-02 2.50e+03 pdb=" C8 A 2 60 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A 2 60 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A 2 60 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 2 60 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A 2 60 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A 2 60 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 2 60 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 2 60 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 2 60 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 669 " -0.031 2.00e-02 2.50e+03 1.40e-02 5.40e+00 pdb=" N9 A 2 669 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A 2 669 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A 2 669 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 2 669 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A 2 669 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 2 669 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 2 669 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 2 669 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A 2 669 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A 2 669 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 918 " 0.029 2.00e-02 2.50e+03 1.53e-02 5.26e+00 pdb=" N1 U 2 918 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U 2 918 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U 2 918 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U 2 918 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U 2 918 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U 2 918 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U 2 918 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U 2 918 " -0.006 2.00e-02 2.50e+03 ... (remaining 5353 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 317 2.57 - 3.15: 35949 3.15 - 3.74: 87893 3.74 - 4.32: 129074 4.32 - 4.90: 181667 Nonbonded interactions: 434900 Sorted by model distance: nonbonded pdb=" OP1 G 21837 " pdb="MG MG 21936 " model vdw 1.989 2.170 nonbonded pdb=" N4 C 21842 " pdb="MG MG 21915 " model vdw 2.003 2.250 nonbonded pdb=" OP2 U 2 100 " pdb="MG MG 21920 " model vdw 2.034 2.170 nonbonded pdb=" OP2 A 2 594 " pdb="MG MG 21962 " model vdw 2.044 2.170 nonbonded pdb=" OE1 GLN G 177 " pdb="MG MG 22004 " model vdw 2.063 2.170 ... (remaining 434895 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 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: 11.370 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: 39.770 Check model and map are aligned: 0.830 Set scattering table: 0.490 Process input model: 161.490 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 226.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.003 0.029 53603 Z= 0.156 Angle : 0.521 9.177 78258 Z= 0.288 Chirality : 0.034 0.244 9728 Planarity : 0.004 0.052 5356 Dihedral : 21.494 179.848 28709 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.48 % Allowed : 3.51 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 0.55 (0.15), residues: 2928 helix: 1.31 (0.17), residues: 937 sheet: 0.09 (0.21), residues: 562 loop : -0.05 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 45 HIS 0.005 0.001 HIS Y 89 PHE 0.015 0.001 PHE J 147 TYR 0.010 0.001 TYR X 134 ARG 0.004 0.001 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 485 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8223 (mp10) REVERT: A 40 LYS cc_start: 0.8303 (tttt) cc_final: 0.8095 (tttm) REVERT: A 126 ASP cc_start: 0.8499 (t0) cc_final: 0.8169 (t0) REVERT: A 130 ASP cc_start: 0.8603 (m-30) cc_final: 0.8148 (m-30) REVERT: A 174 MET cc_start: 0.8263 (mmm) cc_final: 0.7936 (mmm) REVERT: B 177 GLN cc_start: 0.8360 (pt0) cc_final: 0.8130 (pt0) REVERT: C 227 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8197 (ttm170) REVERT: E 79 ASP cc_start: 0.8024 (t0) cc_final: 0.7790 (t0) REVERT: E 104 ASP cc_start: 0.8095 (p0) cc_final: 0.7846 (p0) REVERT: G 146 ASN cc_start: 0.7379 (m-40) cc_final: 0.7155 (m110) REVERT: H 99 ARG cc_start: 0.7574 (mtp180) cc_final: 0.6655 (tpt-90) REVERT: N 19 ARG cc_start: 0.7490 (ptp-170) cc_final: 0.7074 (ppt170) REVERT: R 126 MET cc_start: 0.5236 (ptp) cc_final: 0.4761 (ptp) REVERT: Y 48 TYR cc_start: 0.9015 (m-80) cc_final: 0.8790 (m-80) REVERT: a 19 GLN cc_start: 0.7167 (pm20) cc_final: 0.6953 (pm20) outliers start: 38 outliers final: 11 residues processed: 515 average time/residue: 1.9756 time to fit residues: 1224.2122 Evaluate side-chains 393 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 381 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 84 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 210 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 chunk 322 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 374 optimal weight: 7.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN C 113 GLN H 186 ASN I 146 GLN L 39 ASN O 83 GLN W 56 HIS X 61 GLN Y 106 GLN a 43 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 53603 Z= 0.355 Angle : 0.640 10.786 78258 Z= 0.327 Chirality : 0.042 0.261 9728 Planarity : 0.005 0.056 5356 Dihedral : 23.043 178.382 22497 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.71 % Allowed : 9.59 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 2928 helix: 1.27 (0.17), residues: 959 sheet: 0.07 (0.21), residues: 551 loop : -0.22 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 30 HIS 0.009 0.001 HIS I 22 PHE 0.024 0.002 PHE J 147 TYR 0.016 0.002 TYR X 134 ARG 0.008 0.001 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 375 time to evaluate : 4.069 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8209 (mp10) REVERT: A 40 LYS cc_start: 0.8341 (tttt) cc_final: 0.8136 (tttm) REVERT: B 177 GLN cc_start: 0.8298 (pt0) cc_final: 0.8056 (pt0) REVERT: C 105 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: C 146 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: E 79 ASP cc_start: 0.8293 (t0) cc_final: 0.8074 (t0) REVERT: G 146 ASN cc_start: 0.7625 (m-40) cc_final: 0.7384 (m110) REVERT: H 99 ARG cc_start: 0.7690 (mtp180) cc_final: 0.6716 (tpt170) REVERT: H 113 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.5606 (mtpt) REVERT: I 19 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.7996 (mtmp) REVERT: I 165 GLN cc_start: 0.8648 (mt0) cc_final: 0.8263 (mt0) REVERT: J 154 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: R 126 MET cc_start: 0.5662 (ptp) cc_final: 0.5129 (ptp) REVERT: V 49 GLN cc_start: 0.7318 (mm110) cc_final: 0.6987 (mm110) REVERT: W 98 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: Y 109 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: a 19 GLN cc_start: 0.7272 (pm20) cc_final: 0.7057 (pm20) REVERT: a 21 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8547 (pp) outliers start: 95 outliers final: 43 residues processed: 433 average time/residue: 1.9149 time to fit residues: 1005.2977 Evaluate side-chains 408 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 357 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 118 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 374 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 333 optimal weight: 0.8980 chunk 371 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 300 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS H 76 GLN H 186 ASN I 167 GLN O 83 GLN O 103 ASN V 47 ASN a 43 ASN b 19 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 53603 Z= 0.180 Angle : 0.530 10.875 78258 Z= 0.273 Chirality : 0.036 0.252 9728 Planarity : 0.004 0.053 5356 Dihedral : 22.939 178.325 22491 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.08 % Allowed : 11.39 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 0.64 (0.15), residues: 2928 helix: 1.56 (0.17), residues: 959 sheet: 0.11 (0.21), residues: 551 loop : -0.15 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 139 HIS 0.004 0.001 HIS I 22 PHE 0.016 0.001 PHE J 147 TYR 0.012 0.001 TYR X 134 ARG 0.005 0.000 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 369 time to evaluate : 3.787 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8201 (mp10) REVERT: A 40 LYS cc_start: 0.8337 (tttt) cc_final: 0.8121 (tttm) REVERT: B 177 GLN cc_start: 0.8298 (pt0) cc_final: 0.8078 (pt0) REVERT: C 105 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: E 79 ASP cc_start: 0.8126 (t0) cc_final: 0.7871 (t0) REVERT: E 104 ASP cc_start: 0.8100 (p0) cc_final: 0.7778 (p0) REVERT: E 191 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8431 (mtt180) REVERT: E 199 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7224 (mt-10) REVERT: G 146 ASN cc_start: 0.7545 (m-40) cc_final: 0.7275 (m110) REVERT: H 78 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5446 (mmp-170) REVERT: H 99 ARG cc_start: 0.7660 (mtp180) cc_final: 0.6627 (tpt170) REVERT: H 113 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.5612 (mtpt) REVERT: J 154 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: N 19 ARG cc_start: 0.7483 (ptp-170) cc_final: 0.7175 (ppt170) REVERT: V 49 GLN cc_start: 0.7321 (mm110) cc_final: 0.7000 (mm110) REVERT: X 53 GLU cc_start: 0.7927 (pt0) cc_final: 0.7653 (pt0) REVERT: Y 109 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: a 21 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8525 (pp) REVERT: h 14 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8214 (ttpt) outliers start: 79 outliers final: 39 residues processed: 416 average time/residue: 1.9443 time to fit residues: 983.2312 Evaluate side-chains 402 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 356 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain e residue 24 LYS Chi-restraints excluded: chain e residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 376 optimal weight: 3.9990 chunk 398 optimal weight: 9.9990 chunk 196 optimal weight: 0.0980 chunk 356 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN I 167 GLN O 103 ASN Y 22 GLN a 43 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 53603 Z= 0.252 Angle : 0.568 11.564 78258 Z= 0.292 Chirality : 0.038 0.257 9728 Planarity : 0.005 0.054 5356 Dihedral : 22.899 177.854 22491 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.21 % Allowed : 11.54 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 2928 helix: 1.57 (0.17), residues: 959 sheet: 0.04 (0.21), residues: 562 loop : -0.18 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 139 HIS 0.006 0.001 HIS I 22 PHE 0.021 0.002 PHE J 147 TYR 0.013 0.001 TYR X 134 ARG 0.007 0.000 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 369 time to evaluate : 4.455 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8195 (mp10) REVERT: A 40 LYS cc_start: 0.8374 (tttt) cc_final: 0.8154 (tttm) REVERT: A 198 MET cc_start: 0.7136 (ptm) cc_final: 0.6889 (ttp) REVERT: C 105 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: C 117 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7131 (ttm-80) REVERT: E 79 ASP cc_start: 0.8200 (t0) cc_final: 0.7926 (t0) REVERT: E 104 ASP cc_start: 0.8135 (p0) cc_final: 0.7817 (p0) REVERT: E 191 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8433 (mtt180) REVERT: E 199 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7288 (mt-10) REVERT: G 146 ASN cc_start: 0.7554 (m-40) cc_final: 0.7267 (m110) REVERT: H 64 VAL cc_start: 0.6759 (OUTLIER) cc_final: 0.6545 (p) REVERT: H 99 ARG cc_start: 0.7620 (mtp180) cc_final: 0.6589 (tpt170) REVERT: H 113 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.5734 (mtpt) REVERT: J 154 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: L 97 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7802 (ttm-80) REVERT: V 49 GLN cc_start: 0.7332 (mm110) cc_final: 0.7020 (mm110) REVERT: W 98 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: W 114 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: X 53 GLU cc_start: 0.7958 (pt0) cc_final: 0.7673 (pt0) REVERT: Y 109 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: a 21 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8549 (pp) REVERT: h 10 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7087 (tpp) REVERT: h 14 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8244 (ttpt) outliers start: 108 outliers final: 54 residues processed: 436 average time/residue: 1.9514 time to fit residues: 1035.9758 Evaluate side-chains 427 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 362 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain e residue 22 GLN Chi-restraints excluded: chain e residue 24 LYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain h residue 10 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 339 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 88 ASN I 167 GLN L 112 HIS O 103 ASN R 127 ASN a 43 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 53603 Z= 0.433 Angle : 0.695 12.363 78258 Z= 0.354 Chirality : 0.045 0.283 9728 Planarity : 0.006 0.064 5356 Dihedral : 23.053 178.098 22491 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.33 % Allowed : 12.60 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2928 helix: 1.26 (0.17), residues: 960 sheet: -0.03 (0.21), residues: 537 loop : -0.38 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 139 HIS 0.010 0.002 HIS I 22 PHE 0.026 0.002 PHE J 147 TYR 0.016 0.002 TYR X 134 ARG 0.005 0.001 ARG I 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 367 time to evaluate : 6.556 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8170 (mp10) REVERT: A 40 LYS cc_start: 0.8411 (tttt) cc_final: 0.8154 (tttm) REVERT: A 77 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 25 PHE cc_start: 0.7193 (m-80) cc_final: 0.6944 (m-80) REVERT: C 105 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: C 117 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7132 (ttm-80) REVERT: E 191 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8450 (mtt180) REVERT: E 199 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7309 (mt-10) REVERT: G 146 ASN cc_start: 0.7643 (m-40) cc_final: 0.7398 (m110) REVERT: H 99 ARG cc_start: 0.7699 (mtp180) cc_final: 0.6605 (tpt170) REVERT: H 113 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.5756 (mtpt) REVERT: I 99 ASN cc_start: 0.8602 (t0) cc_final: 0.8118 (t160) REVERT: J 154 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: O 88 LEU cc_start: 0.7896 (mt) cc_final: 0.7691 (mt) REVERT: O 121 ARG cc_start: 0.6941 (mmt90) cc_final: 0.6679 (mmm-85) REVERT: V 49 GLN cc_start: 0.7355 (mm110) cc_final: 0.6973 (mm110) REVERT: W 98 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: Y 109 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: a 21 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8611 (pp) REVERT: b 16 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8443 (tmtp) REVERT: h 10 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7061 (tpp) REVERT: h 14 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8335 (ttpt) outliers start: 111 outliers final: 62 residues processed: 435 average time/residue: 1.9472 time to fit residues: 1027.2801 Evaluate side-chains 421 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 349 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 99 GLU Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain e residue 24 LYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain h residue 10 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 2.9990 chunk 358 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 233 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 398 optimal weight: 6.9990 chunk 330 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 209 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 167 GLN O 83 GLN O 103 ASN R 127 ASN a 43 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 53603 Z= 0.120 Angle : 0.513 12.158 78258 Z= 0.264 Chirality : 0.034 0.257 9728 Planarity : 0.004 0.051 5356 Dihedral : 22.874 179.389 22491 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.81 % Allowed : 14.59 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 0.70 (0.15), residues: 2928 helix: 1.69 (0.17), residues: 961 sheet: 0.14 (0.21), residues: 546 loop : -0.18 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 139 HIS 0.003 0.001 HIS X 23 PHE 0.012 0.001 PHE J 147 TYR 0.013 0.001 TYR I 21 ARG 0.006 0.000 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 363 time to evaluate : 3.444 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8368 (tttt) cc_final: 0.8159 (tttm) REVERT: A 198 MET cc_start: 0.6835 (ttp) cc_final: 0.6458 (ttp) REVERT: C 105 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: C 117 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7075 (ttm-80) REVERT: E 79 ASP cc_start: 0.8096 (t0) cc_final: 0.7860 (t0) REVERT: E 104 ASP cc_start: 0.8141 (p0) cc_final: 0.7839 (p0) REVERT: E 191 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8420 (mtt180) REVERT: E 199 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7315 (mt-10) REVERT: G 22 ARG cc_start: 0.7125 (mtm180) cc_final: 0.6909 (mtm180) REVERT: G 146 ASN cc_start: 0.7534 (m-40) cc_final: 0.7248 (m110) REVERT: H 58 LYS cc_start: 0.6706 (mppt) cc_final: 0.6271 (mmtt) REVERT: H 99 ARG cc_start: 0.7610 (mtp180) cc_final: 0.6563 (tpt170) REVERT: H 113 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.5543 (mtpt) REVERT: V 49 GLN cc_start: 0.7400 (mm110) cc_final: 0.7037 (mm110) REVERT: W 114 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: X 53 GLU cc_start: 0.7869 (pt0) cc_final: 0.7584 (pt0) REVERT: Y 109 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: b 16 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8408 (tttp) REVERT: h 10 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.7015 (tpp) REVERT: h 14 LYS cc_start: 0.8429 (ttmt) cc_final: 0.8202 (ttpt) outliers start: 72 outliers final: 38 residues processed: 411 average time/residue: 1.9046 time to fit residues: 949.6691 Evaluate side-chains 399 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 354 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain e residue 24 LYS Chi-restraints excluded: chain h residue 10 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 335 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 397 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN N 13 GLN O 83 GLN O 103 ASN a 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 53603 Z= 0.310 Angle : 0.604 12.247 78258 Z= 0.309 Chirality : 0.040 0.273 9728 Planarity : 0.005 0.054 5356 Dihedral : 22.859 178.620 22489 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.71 % Allowed : 14.66 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 2928 helix: 1.56 (0.17), residues: 961 sheet: 0.08 (0.21), residues: 541 loop : -0.23 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 139 HIS 0.007 0.001 HIS I 22 PHE 0.023 0.002 PHE J 147 TYR 0.014 0.002 TYR X 134 ARG 0.007 0.001 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 358 time to evaluate : 4.060 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8432 (tttt) cc_final: 0.8183 (tttm) REVERT: A 198 MET cc_start: 0.6906 (ttp) cc_final: 0.6587 (ttp) REVERT: C 105 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: C 117 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7122 (ttm-80) REVERT: E 79 ASP cc_start: 0.8293 (t0) cc_final: 0.8078 (t0) REVERT: E 191 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8471 (mtt180) REVERT: G 46 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7563 (tttt) REVERT: G 146 ASN cc_start: 0.7449 (m-40) cc_final: 0.7177 (m110) REVERT: H 64 VAL cc_start: 0.6869 (OUTLIER) cc_final: 0.6655 (p) REVERT: H 74 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6279 (tppp) REVERT: H 99 ARG cc_start: 0.7637 (mtp180) cc_final: 0.6566 (tpt170) REVERT: H 113 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.5694 (mtpt) REVERT: J 154 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: L 81 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8215 (mttm) REVERT: V 49 GLN cc_start: 0.7365 (mm110) cc_final: 0.7002 (mm110) REVERT: W 114 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: Y 109 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: h 10 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.7029 (tpp) REVERT: h 14 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8235 (ttpt) outliers start: 95 outliers final: 59 residues processed: 417 average time/residue: 1.9679 time to fit residues: 995.6069 Evaluate side-chains 424 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 354 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 99 GLU Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 120 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain e residue 24 LYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain h residue 10 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 237 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 HIS ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN O 83 GLN O 103 ASN a 43 ASN j 158 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 53603 Z= 0.198 Angle : 0.551 12.316 78258 Z= 0.285 Chirality : 0.037 0.268 9728 Planarity : 0.004 0.053 5356 Dihedral : 22.859 177.866 22489 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.28 % Allowed : 15.37 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 2928 helix: 1.64 (0.17), residues: 961 sheet: 0.10 (0.21), residues: 541 loop : -0.21 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 139 HIS 0.005 0.001 HIS I 22 PHE 0.020 0.001 PHE J 147 TYR 0.013 0.001 TYR X 134 ARG 0.007 0.000 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 357 time to evaluate : 3.754 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8426 (tttt) cc_final: 0.8183 (tttm) REVERT: A 198 MET cc_start: 0.6948 (ttp) cc_final: 0.6619 (ttp) REVERT: C 105 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: C 117 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7126 (ttm-80) REVERT: E 79 ASP cc_start: 0.8210 (t0) cc_final: 0.8006 (t0) REVERT: E 191 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8478 (mtt180) REVERT: G 146 ASN cc_start: 0.7441 (m-40) cc_final: 0.7164 (m110) REVERT: H 58 LYS cc_start: 0.6775 (mppt) cc_final: 0.6384 (mmtt) REVERT: H 64 VAL cc_start: 0.6853 (OUTLIER) cc_final: 0.6642 (p) REVERT: H 74 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6273 (tppp) REVERT: H 99 ARG cc_start: 0.7626 (mtp180) cc_final: 0.6560 (tpt170) REVERT: H 113 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.5687 (mtpt) REVERT: L 81 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8194 (mttm) REVERT: O 88 LEU cc_start: 0.7668 (mt) cc_final: 0.7389 (mt) REVERT: V 49 GLN cc_start: 0.7363 (mm110) cc_final: 0.7007 (mm110) REVERT: W 114 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: X 53 GLU cc_start: 0.7944 (pt0) cc_final: 0.7646 (pt0) REVERT: X 87 ASN cc_start: 0.8049 (m-40) cc_final: 0.7793 (m-40) REVERT: Y 109 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: a 21 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8545 (pp) REVERT: h 10 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7049 (tpp) REVERT: h 14 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8188 (ttpt) outliers start: 84 outliers final: 56 residues processed: 413 average time/residue: 1.9889 time to fit residues: 992.1116 Evaluate side-chains 419 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 353 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 99 GLU Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain e residue 24 LYS Chi-restraints excluded: chain h residue 10 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 0.9980 chunk 380 optimal weight: 2.9990 chunk 347 optimal weight: 0.9980 chunk 370 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 334 optimal weight: 1.9990 chunk 349 optimal weight: 2.9990 chunk 368 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN O 83 GLN O 103 ASN a 43 ASN j 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 53603 Z= 0.209 Angle : 0.547 12.366 78258 Z= 0.282 Chirality : 0.037 0.265 9728 Planarity : 0.004 0.054 5356 Dihedral : 22.794 177.995 22489 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.24 % Allowed : 15.64 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 2928 helix: 1.66 (0.17), residues: 962 sheet: 0.14 (0.21), residues: 550 loop : -0.22 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 139 HIS 0.005 0.001 HIS I 22 PHE 0.019 0.001 PHE J 147 TYR 0.013 0.001 TYR X 134 ARG 0.007 0.000 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 360 time to evaluate : 3.608 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8429 (tttt) cc_final: 0.8189 (tttm) REVERT: A 198 MET cc_start: 0.6971 (ttp) cc_final: 0.6636 (ttp) REVERT: C 105 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: C 117 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7114 (ttm-80) REVERT: E 79 ASP cc_start: 0.8186 (t0) cc_final: 0.7915 (t0) REVERT: E 104 ASP cc_start: 0.8105 (p0) cc_final: 0.7800 (p0) REVERT: E 191 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8475 (mtt180) REVERT: G 46 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7543 (tttt) REVERT: G 146 ASN cc_start: 0.7433 (m-40) cc_final: 0.7145 (m110) REVERT: H 64 VAL cc_start: 0.6773 (OUTLIER) cc_final: 0.6572 (p) REVERT: H 74 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6238 (tppp) REVERT: H 99 ARG cc_start: 0.7613 (mtp180) cc_final: 0.6567 (tpt170) REVERT: H 113 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.5703 (mtpt) REVERT: J 154 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: L 81 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8202 (mttm) REVERT: V 49 GLN cc_start: 0.7365 (mm110) cc_final: 0.7013 (mm110) REVERT: W 98 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: W 114 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: Y 109 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: a 21 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8526 (pp) REVERT: h 10 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.7013 (tpp) outliers start: 83 outliers final: 56 residues processed: 412 average time/residue: 1.9730 time to fit residues: 983.6700 Evaluate side-chains 426 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 357 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 99 GLU Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain e residue 24 LYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain h residue 10 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 8.9990 chunk 391 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 185 optimal weight: 0.0570 chunk 272 optimal weight: 0.7980 chunk 410 optimal weight: 0.8980 chunk 377 optimal weight: 0.8980 chunk 326 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 200 optimal weight: 0.0470 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN I 167 GLN O 83 GLN O 103 ASN a 43 ASN j 158 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 53603 Z= 0.122 Angle : 0.525 12.122 78258 Z= 0.270 Chirality : 0.035 0.264 9728 Planarity : 0.004 0.051 5356 Dihedral : 22.810 178.441 22489 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.57 % Allowed : 16.30 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 2928 helix: 1.81 (0.17), residues: 962 sheet: 0.16 (0.21), residues: 537 loop : -0.17 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 139 HIS 0.003 0.001 HIS Y 89 PHE 0.017 0.001 PHE J 147 TYR 0.012 0.001 TYR L 37 ARG 0.009 0.000 ARG I 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 360 time to evaluate : 3.620 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8427 (tttt) cc_final: 0.8185 (tttm) REVERT: A 198 MET cc_start: 0.6927 (ttp) cc_final: 0.6574 (ttp) REVERT: C 105 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: C 117 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7088 (ttm-80) REVERT: E 79 ASP cc_start: 0.8138 (t0) cc_final: 0.7865 (t0) REVERT: E 104 ASP cc_start: 0.8112 (p0) cc_final: 0.7818 (p0) REVERT: E 191 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8466 (mtt180) REVERT: G 46 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7562 (tttt) REVERT: G 146 ASN cc_start: 0.7406 (m-40) cc_final: 0.7097 (m110) REVERT: H 58 LYS cc_start: 0.6711 (mppt) cc_final: 0.6347 (mmtt) REVERT: H 74 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6177 (tppp) REVERT: H 99 ARG cc_start: 0.7599 (mtp180) cc_final: 0.6609 (tpt-90) REVERT: H 109 ARG cc_start: 0.2893 (OUTLIER) cc_final: 0.1844 (ptm-80) REVERT: H 113 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.5736 (mtpt) REVERT: J 154 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: L 81 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8152 (mttm) REVERT: V 49 GLN cc_start: 0.7359 (mm110) cc_final: 0.7010 (mm110) REVERT: W 114 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: X 53 GLU cc_start: 0.7895 (pt0) cc_final: 0.7599 (pt0) REVERT: Y 109 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: a 21 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8493 (pp) outliers start: 66 outliers final: 47 residues processed: 408 average time/residue: 1.9925 time to fit residues: 982.4377 Evaluate side-chains 415 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 357 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain e residue 24 LYS Chi-restraints excluded: chain e residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 4.9990 chunk 348 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 336 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN O 103 ASN a 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101810 restraints weight = 54471.571| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 0.92 r_work: 0.2695 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 53603 Z= 0.310 Angle : 0.602 12.518 78258 Z= 0.309 Chirality : 0.040 0.274 9728 Planarity : 0.005 0.055 5356 Dihedral : 22.800 178.056 22489 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.89 % Allowed : 15.87 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 2928 helix: 1.61 (0.17), residues: 961 sheet: 0.13 (0.21), residues: 535 loop : -0.27 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 139 HIS 0.007 0.001 HIS I 22 PHE 0.023 0.002 PHE J 147 TYR 0.014 0.002 TYR Y 48 ARG 0.006 0.000 ARG E 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15753.08 seconds wall clock time: 281 minutes 13.17 seconds (16873.17 seconds total)