Starting phenix.real_space_refine on Wed Mar 20 05:03:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls5_23502/03_2024/7ls5_23502.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls5_23502/03_2024/7ls5_23502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls5_23502/03_2024/7ls5_23502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls5_23502/03_2024/7ls5_23502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls5_23502/03_2024/7ls5_23502.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls5_23502/03_2024/7ls5_23502.pdb" } resolution = 2.74 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= 0.004 sd= 0.079 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: 5 Type Number sf(0) Gaussians S 155 5.16 5 C 31105 2.51 5 N 8343 2.21 5 O 9544 1.98 5 H 48895 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "I PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "I GLU 197": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K GLU 114": "OE1" <-> "OE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "L GLU 112": "OE1" <-> "OE2" Residue "L GLU 227": "OE1" <-> "OE2" Residue "M GLU 179": "OE1" <-> "OE2" Residue "M GLU 193": "OE1" <-> "OE2" Residue "M GLU 215": "OE1" <-> "OE2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "N GLU 174": "OE1" <-> "OE2" Residue "N GLU 175": "OE1" <-> "OE2" Residue "P GLU 182": "OE1" <-> "OE2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q GLU 224": "OE1" <-> "OE2" Residue "R GLU 21": "OE1" <-> "OE2" Residue "R GLU 151": "OE1" <-> "OE2" Residue "R GLU 183": "OE1" <-> "OE2" Residue "S TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 177": "OE1" <-> "OE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S GLU 214": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T GLU 173": "OE1" <-> "OE2" Residue "T GLU 188": "OE1" <-> "OE2" Residue "U GLU 190": "OE1" <-> "OE2" Residue "U GLU 214": "OE1" <-> "OE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V GLU 109": "OE1" <-> "OE2" Residue "W PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 185": "OE1" <-> "OE2" Residue "W GLU 197": "OE1" <-> "OE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "Y GLU 57": "OE1" <-> "OE2" Residue "Y GLU 73": "OE1" <-> "OE2" Residue "Y GLU 168": "OE1" <-> "OE2" Residue "Z GLU 112": "OE1" <-> "OE2" Residue "1 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 GLU 178": "OE1" <-> "OE2" Residue "1 GLU 193": "OE1" <-> "OE2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "2 GLU 40": "OE1" <-> "OE2" Residue "2 GLU 73": "OE1" <-> "OE2" Residue "2 GLU 94": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 98042 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3832 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 10, 'TRANS': 232} Chain: "B" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3845 Classifications: {'peptide': 250} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "C" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3754 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "D" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3735 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 2 Chain: "E" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3609 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 4, 'TRANS': 230} Chain breaks: 1 Chain: "F" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3551 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "G" Number of atoms: 3784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3784 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 9, 'TRANS': 234} Chain: "H" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 2996 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "I" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3347 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain: "J" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3153 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3111 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "L" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3237 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "M" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3467 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "N" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3654 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "O" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3793 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 10, 'TRANS': 229} Chain: "P" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3776 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 233} Chain: "Q" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3806 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "R" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3694 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 2 Chain: "S" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3616 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 4, 'TRANS': 231} Chain breaks: 1 Chain: "T" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3551 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "U" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3777 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "V" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 2996 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "W" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3347 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain: "X" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3142 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "Y" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3112 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "Z" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3237 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "1" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3466 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "2" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3654 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Time building chain proxies: 32.19, per 1000 atoms: 0.33 Number of scatterers: 98042 At special positions: 0 Unit cell: (145.22, 179.14, 142.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 155 16.00 O 9544 8.00 N 8343 7.00 C 31105 6.00 H 48895 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 71.01 Conformation dependent library (CDL) restraints added in 8.1 seconds 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11602 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 70 sheets defined 40.7% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.86 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.506A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 131 Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.534A pdb=" N ASN A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.511A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.582A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.626A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 7 removed outlier: 3.539A pdb=" N ASP C 7 " --> pdb=" O ARG C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.554A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.560A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'D' and resid 17 through 30 Processing helix chain 'D' and resid 78 through 101 removed outlier: 3.766A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.624A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 203 removed outlier: 4.073A pdb=" N VAL D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 243 Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.634A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.706A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 removed outlier: 3.735A pdb=" N LEU E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU E 121 " --> pdb=" O CYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 187 removed outlier: 3.687A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 208 removed outlier: 3.510A pdb=" N GLN E 206 " --> pdb=" O LYS E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 250 Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.691A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.574A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 175 removed outlier: 4.158A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 185 through 198 removed outlier: 3.582A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 107 through 122 Processing helix chain 'G' and resid 167 through 182 removed outlier: 3.558A pdb=" N ALA G 173 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 203 Processing helix chain 'G' and resid 204 through 207 removed outlier: 4.036A pdb=" N LYS G 207 " --> pdb=" O GLU G 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 204 through 207' Processing helix chain 'G' and resid 220 through 224 Processing helix chain 'G' and resid 232 through 247 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 74 through 89 Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.629A pdb=" N THR H 132 " --> pdb=" O SER H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 142 Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'H' and resid 189 through 194 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.573A pdb=" N TYR I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.669A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 55 through 78 Processing helix chain 'J' and resid 82 through 96 Processing helix chain 'J' and resid 141 through 153 Processing helix chain 'J' and resid 158 through 176 removed outlier: 3.641A pdb=" N GLU J 164 " --> pdb=" O GLU J 160 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG J 176 " --> pdb=" O ASN J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 71 Processing helix chain 'K' and resid 75 through 92 removed outlier: 4.153A pdb=" N ARG K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 147 removed outlier: 3.820A pdb=" N TYR K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR K 139 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU K 142 " --> pdb=" O TYR K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 124 through 147 removed outlier: 3.662A pdb=" N SER L 137 " --> pdb=" O THR L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 166 Processing helix chain 'L' and resid 208 through 220 removed outlier: 3.551A pdb=" N VAL L 215 " --> pdb=" O PHE L 211 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER L 218 " --> pdb=" O GLY L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 244 Processing helix chain 'L' and resid 269 through 281 removed outlier: 3.915A pdb=" N TRP L 274 " --> pdb=" O GLY L 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 79 Processing helix chain 'M' and resid 85 through 99 Processing helix chain 'M' and resid 142 through 155 Proline residue: M 148 - end of helix Processing helix chain 'M' and resid 176 through 195 Processing helix chain 'N' and resid 57 through 76 removed outlier: 3.579A pdb=" N ALA N 75 " --> pdb=" O VAL N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 106 Processing helix chain 'N' and resid 146 through 159 removed outlier: 3.685A pdb=" N MET N 150 " --> pdb=" O PHE N 146 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN N 152 " --> pdb=" O ALA N 148 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.744A pdb=" N LYS N 157 " --> pdb=" O PRO N 153 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL N 158 " --> pdb=" O LEU N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 168 Proline residue: N 166 - end of helix Processing helix chain 'N' and resid 169 through 188 Processing helix chain 'N' and resid 219 through 225 removed outlier: 3.865A pdb=" N LYS N 223 " --> pdb=" O ASP N 220 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP N 224 " --> pdb=" O PHE N 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 15 removed outlier: 3.743A pdb=" N ARG O 14 " --> pdb=" O GLY O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 36 removed outlier: 3.500A pdb=" N LYS O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN O 36 " --> pdb=" O PHE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 65 through 69 Processing helix chain 'O' and resid 86 through 109 Processing helix chain 'O' and resid 113 through 131 Processing helix chain 'O' and resid 174 through 190 Processing helix chain 'O' and resid 198 through 215 Processing helix chain 'O' and resid 237 through 250 Processing helix chain 'P' and resid 18 through 30 Processing helix chain 'P' and resid 58 through 61 Processing helix chain 'P' and resid 78 through 96 Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'P' and resid 167 through 179 Processing helix chain 'P' and resid 184 through 200 removed outlier: 3.573A pdb=" N SER P 199 " --> pdb=" O THR P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 222 Processing helix chain 'P' and resid 239 through 249 removed outlier: 3.634A pdb=" N ALA P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 removed outlier: 3.710A pdb=" N ARG Q 5 " --> pdb=" O GLY Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 30 Processing helix chain 'Q' and resid 80 through 103 removed outlier: 3.576A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 125 removed outlier: 3.562A pdb=" N TYR Q 122 " --> pdb=" O ILE Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 Processing helix chain 'Q' and resid 185 through 201 Processing helix chain 'Q' and resid 207 through 209 No H-bonds generated for 'chain 'Q' and resid 207 through 209' Processing helix chain 'Q' and resid 231 through 242 Processing helix chain 'R' and resid 17 through 30 Processing helix chain 'R' and resid 78 through 101 removed outlier: 3.756A pdb=" N ILE R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 120 Processing helix chain 'R' and resid 167 through 179 removed outlier: 3.621A pdb=" N LYS R 177 " --> pdb=" O GLU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 203 removed outlier: 4.068A pdb=" N VAL R 202 " --> pdb=" O SER R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 243 Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.625A pdb=" N LYS S 32 " --> pdb=" O LEU S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 removed outlier: 3.708A pdb=" N ALA S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG S 86 " --> pdb=" O THR S 82 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 121 removed outlier: 3.739A pdb=" N LEU S 119 " --> pdb=" O SER S 115 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA S 120 " --> pdb=" O VAL S 116 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU S 121 " --> pdb=" O CYS S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 187 removed outlier: 3.693A pdb=" N ALA S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 208 removed outlier: 3.512A pdb=" N GLN S 206 " --> pdb=" O LYS S 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 250 Processing helix chain 'T' and resid 19 through 32 removed outlier: 3.695A pdb=" N ILE T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS T 30 " --> pdb=" O LEU T 26 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 100 Processing helix chain 'T' and resid 104 through 119 removed outlier: 3.571A pdb=" N LYS T 118 " --> pdb=" O ASP T 114 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 175 removed outlier: 4.152A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 175 through 180 Processing helix chain 'T' and resid 185 through 198 removed outlier: 3.582A pdb=" N LEU T 189 " --> pdb=" O ASN T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 201 No H-bonds generated for 'chain 'T' and resid 199 through 201' Processing helix chain 'T' and resid 228 through 231 Processing helix chain 'U' and resid 20 through 31 Processing helix chain 'U' and resid 80 through 103 Processing helix chain 'U' and resid 107 through 122 Processing helix chain 'U' and resid 167 through 182 removed outlier: 3.548A pdb=" N ALA U 173 " --> pdb=" O GLN U 169 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU U 174 " --> pdb=" O SER U 170 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 203 Processing helix chain 'U' and resid 204 through 207 removed outlier: 4.032A pdb=" N LYS U 207 " --> pdb=" O GLU U 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 204 through 207' Processing helix chain 'U' and resid 220 through 224 Processing helix chain 'U' and resid 232 through 247 Processing helix chain 'V' and resid 48 through 71 removed outlier: 3.547A pdb=" N GLN V 69 " --> pdb=" O LEU V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 89 Processing helix chain 'V' and resid 128 through 133 removed outlier: 3.645A pdb=" N THR V 132 " --> pdb=" O SER V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 142 Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'V' and resid 189 through 194 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.567A pdb=" N TYR W 90 " --> pdb=" O HIS W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.626A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'X' and resid 2 through 6 Processing helix chain 'X' and resid 55 through 78 Processing helix chain 'X' and resid 82 through 96 removed outlier: 3.526A pdb=" N GLN X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 153 Processing helix chain 'X' and resid 158 through 176 removed outlier: 3.639A pdb=" N GLU X 164 " --> pdb=" O GLU X 160 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG X 176 " --> pdb=" O ASN X 172 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 71 Processing helix chain 'Y' and resid 75 through 92 removed outlier: 4.150A pdb=" N ARG Y 92 " --> pdb=" O ALA Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 147 removed outlier: 3.922A pdb=" N TYR Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR Y 139 " --> pdb=" O SER Y 135 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU Y 142 " --> pdb=" O TYR Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 Processing helix chain 'Z' and resid 124 through 147 removed outlier: 3.671A pdb=" N SER Z 137 " --> pdb=" O THR Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 151 through 166 Processing helix chain 'Z' and resid 208 through 220 removed outlier: 3.536A pdb=" N VAL Z 215 " --> pdb=" O PHE Z 211 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER Z 218 " --> pdb=" O GLY Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 225 through 244 Processing helix chain 'Z' and resid 269 through 281 removed outlier: 3.911A pdb=" N TRP Z 274 " --> pdb=" O GLY Z 270 " (cutoff:3.500A) Processing helix chain '1' and resid 57 through 79 Processing helix chain '1' and resid 85 through 99 Processing helix chain '1' and resid 142 through 155 Proline residue: 1 148 - end of helix Processing helix chain '1' and resid 176 through 195 Processing helix chain '2' and resid 57 through 76 removed outlier: 3.575A pdb=" N ALA 2 75 " --> pdb=" O VAL 2 71 " (cutoff:3.500A) Processing helix chain '2' and resid 88 through 106 Processing helix chain '2' and resid 146 through 159 removed outlier: 3.704A pdb=" N MET 2 150 " --> pdb=" O PHE 2 146 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASN 2 152 " --> pdb=" O ALA 2 148 " (cutoff:3.500A) Proline residue: 2 153 - end of helix removed outlier: 3.765A pdb=" N LYS 2 157 " --> pdb=" O PRO 2 153 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 161 through 165 Processing helix chain '2' and resid 169 through 188 Processing helix chain '2' and resid 219 through 225 removed outlier: 3.883A pdb=" N LYS 2 223 " --> pdb=" O ASP 2 220 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP 2 224 " --> pdb=" O PHE 2 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 4.656A pdb=" N VAL A 225 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 73 removed outlier: 4.149A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 164 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY A 165 " --> pdb=" O MET B 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.591A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 211 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.477A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.574A pdb=" N THR B 225 " --> pdb=" O TYR I 186 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG I 188 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN I 189 " --> pdb=" O VAL I 173 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL I 173 " --> pdb=" O ASN I 189 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR I 2 " --> pdb=" O ASP I 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.631A pdb=" N GLY C 43 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 68 removed outlier: 4.096A pdb=" N LEU C 148 " --> pdb=" O TRP C 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AA9, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.292A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB5, first strand: chain 'G' and resid 161 through 164 removed outlier: 4.363A pdb=" N ASP G 210 " --> pdb=" O ILE G 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.668A pdb=" N TRP G 157 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 124 through 127 Processing sheet with id=AB8, first strand: chain 'H' and resid 20 through 22 removed outlier: 7.094A pdb=" N THR H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR H 25 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.486A pdb=" N ILE H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL H 110 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.378A pdb=" N GLN I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL I 26 " --> pdb=" O GLN I 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.468A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR I 97 " --> pdb=" O ALA I 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 212 through 218 removed outlier: 6.667A pdb=" N TYR J 198 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU I 215 " --> pdb=" O LYS J 196 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS J 196 " --> pdb=" O GLU I 215 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE I 217 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL J 194 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.626A pdb=" N LEU J 28 " --> pdb=" O VAL J 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 44 Processing sheet with id=AC6, first strand: chain 'K' and resid 129 through 131 removed outlier: 4.500A pdb=" N VAL K 180 " --> pdb=" O VAL K 191 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.671A pdb=" N ARG K 22 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.308A pdb=" N THR K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 202 through 206 removed outlier: 6.186A pdb=" N VAL L 251 " --> pdb=" O ASN L 266 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN L 266 " --> pdb=" O VAL L 251 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU L 253 " --> pdb=" O HIS L 264 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 96 through 98 removed outlier: 6.783A pdb=" N ALA L 96 " --> pdb=" O ALA L 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 117 through 118 removed outlier: 4.249A pdb=" N ILE L 188 " --> pdb=" O GLY L 200 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 136 through 140 removed outlier: 5.049A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.267A pdb=" N THR M 31 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE M 35 " --> pdb=" O THR M 31 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 44 through 45 removed outlier: 3.605A pdb=" N THR M 109 " --> pdb=" O PHE M 125 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER M 124 " --> pdb=" O GLU M 132 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU M 132 " --> pdb=" O SER M 124 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.476A pdb=" N LEU N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR N 30 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.476A pdb=" N LEU N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR N 30 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 141 through 143 removed outlier: 5.799A pdb=" N PHE N 195 " --> pdb=" O ASN N 211 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN N 211 " --> pdb=" O PHE N 195 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 168 through 171 Processing sheet with id=AE1, first strand: chain 'O' and resid 72 through 73 removed outlier: 4.150A pdb=" N ILE O 154 " --> pdb=" O TYR O 166 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL O 164 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY O 165 " --> pdb=" O MET P 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 161 through 164 removed outlier: 3.591A pdb=" N GLY P 42 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU P 211 " --> pdb=" O LEU P 238 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 65 through 68 removed outlier: 6.479A pdb=" N ILE P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 224 through 225 removed outlier: 6.591A pdb=" N THR P 225 " --> pdb=" O TYR W 186 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG W 188 " --> pdb=" O THR P 225 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN W 189 " --> pdb=" O VAL W 173 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL W 173 " --> pdb=" O ASN W 189 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR W 2 " --> pdb=" O ASP W 17 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 162 through 165 Processing sheet with id=AE6, first strand: chain 'Q' and resid 66 through 68 removed outlier: 4.082A pdb=" N LEU Q 148 " --> pdb=" O TRP Q 160 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 161 through 164 Processing sheet with id=AE8, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AE9, first strand: chain 'S' and resid 169 through 172 Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.295A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF3, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF4, first strand: chain 'U' and resid 161 through 164 removed outlier: 4.393A pdb=" N ASP U 210 " --> pdb=" O ILE U 53 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.506A pdb=" N THR U 135 " --> pdb=" O LEU U 150 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP U 157 " --> pdb=" O MET U 149 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 124 through 127 Processing sheet with id=AF7, first strand: chain 'V' and resid 20 through 22 removed outlier: 7.111A pdb=" N THR V 20 " --> pdb=" O ALA V 27 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR V 25 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.504A pdb=" N ILE V 41 " --> pdb=" O VAL V 37 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL V 110 " --> pdb=" O LEU V 122 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.372A pdb=" N GLN W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL W 26 " --> pdb=" O GLN W 22 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.447A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR W 97 " --> pdb=" O ALA W 46 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 212 through 218 removed outlier: 6.523A pdb=" N TYR X 198 " --> pdb=" O LEU W 213 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU W 215 " --> pdb=" O LYS X 196 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS X 196 " --> pdb=" O GLU W 215 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE W 217 " --> pdb=" O VAL X 194 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL X 194 " --> pdb=" O ILE W 217 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.582A pdb=" N LEU X 28 " --> pdb=" O VAL X 35 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 42 through 44 Processing sheet with id=AG5, first strand: chain 'Y' and resid 129 through 131 removed outlier: 4.493A pdb=" N VAL Y 180 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 20 through 22 removed outlier: 6.652A pdb=" N ARG Y 22 " --> pdb=" O VAL Y 26 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL Y 26 " --> pdb=" O ARG Y 22 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.308A pdb=" N THR Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 202 through 206 removed outlier: 6.184A pdb=" N VAL Z 251 " --> pdb=" O ASN Z 266 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASN Z 266 " --> pdb=" O VAL Z 251 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU Z 253 " --> pdb=" O HIS Z 264 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 96 through 98 removed outlier: 6.795A pdb=" N ALA Z 96 " --> pdb=" O ALA Z 103 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 117 through 118 removed outlier: 4.264A pdb=" N ILE Z 188 " --> pdb=" O GLY Z 200 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '1' and resid 136 through 140 removed outlier: 5.044A pdb=" N THR 1 11 " --> pdb=" O ASP 1 26 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '1' and resid 29 through 31 removed outlier: 6.294A pdb=" N THR 1 31 " --> pdb=" O ILE 1 35 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE 1 35 " --> pdb=" O THR 1 31 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '1' and resid 43 through 45 removed outlier: 3.519A pdb=" N THR 1 109 " --> pdb=" O PHE 1 125 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL 1 122 " --> pdb=" O GLU 1 134 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER 1 124 " --> pdb=" O GLU 1 132 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '2' and resid 33 through 36 removed outlier: 5.483A pdb=" N LEU 2 34 " --> pdb=" O TYR 2 30 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR 2 30 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2' and resid 33 through 36 removed outlier: 5.483A pdb=" N LEU 2 34 " --> pdb=" O TYR 2 30 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR 2 30 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '2' and resid 141 through 143 removed outlier: 5.792A pdb=" N PHE 2 195 " --> pdb=" O ASN 2 211 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN 2 211 " --> pdb=" O PHE 2 195 " (cutoff:3.500A) 2857 hydrogen bonds defined for protein. 8136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 40.03 Time building geometry restraints manager: 74.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 48827 1.03 - 1.23: 87 1.23 - 1.42: 20884 1.42 - 1.61: 28895 1.61 - 1.81: 242 Bond restraints: 98935 Sorted by residual: bond pdb=" N GLY O 11 " pdb=" CA GLY O 11 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.44e+00 bond pdb=" N GLY G 4 " pdb=" CA GLY G 4 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.41e+00 bond pdb=" N PHE H 8 " pdb=" H PHE H 8 " ideal model delta sigma weight residual 0.860 0.909 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" N GLY R 3 " pdb=" CA GLY R 3 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.02e+00 bond pdb=" N GLY Q 2 " pdb=" CA GLY Q 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.80e+00 ... (remaining 98930 not shown) Histogram of bond angle deviations from ideal: 73.56 - 85.65: 48 85.65 - 97.75: 0 97.75 - 109.84: 76778 109.84 - 121.93: 84494 121.93 - 134.02: 17393 Bond angle restraints: 178713 Sorted by residual: angle pdb=" C GLN R 243 " pdb=" CA GLN R 243 " pdb=" HA GLN R 243 " ideal model delta sigma weight residual 109.00 73.56 35.44 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CB LYS R 208 " pdb=" CA LYS R 208 " pdb=" HA LYS R 208 " ideal model delta sigma weight residual 109.00 73.86 35.14 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N LYS R 208 " pdb=" CA LYS R 208 " pdb=" HA LYS R 208 " ideal model delta sigma weight residual 110.00 75.06 34.94 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N THR U 5 " pdb=" CA THR U 5 " pdb=" HA THR U 5 " ideal model delta sigma weight residual 110.00 75.15 34.85 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C THR U 5 " pdb=" CA THR U 5 " pdb=" HA THR U 5 " ideal model delta sigma weight residual 109.00 74.15 34.85 3.00e+00 1.11e-01 1.35e+02 ... (remaining 178708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 42721 17.90 - 35.81: 2489 35.81 - 53.71: 816 53.71 - 71.62: 278 71.62 - 89.52: 122 Dihedral angle restraints: 46426 sinusoidal: 25290 harmonic: 21136 Sorted by residual: dihedral pdb=" CA GLY X 100 " pdb=" C GLY X 100 " pdb=" N PRO X 101 " pdb=" CA PRO X 101 " ideal model delta harmonic sigma weight residual -180.00 -156.75 -23.25 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA GLY J 100 " pdb=" C GLY J 100 " pdb=" N PRO J 101 " pdb=" CA PRO J 101 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LEU C 211 " pdb=" C LEU C 211 " pdb=" N GLU C 212 " pdb=" CA GLU C 212 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 46423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.298: 7618 0.298 - 0.595: 3 0.595 - 0.893: 0 0.893 - 1.190: 0 1.190 - 1.488: 5 Chirality restraints: 7626 Sorted by residual: chirality pdb=" CB THR M 164 " pdb=" CA THR M 164 " pdb=" OG1 THR M 164 " pdb=" CG2 THR M 164 " both_signs ideal model delta sigma weight residual False 2.55 1.06 1.49 2.00e-01 2.50e+01 5.53e+01 chirality pdb=" CB THR G 5 " pdb=" CA THR G 5 " pdb=" OG1 THR G 5 " pdb=" CG2 THR G 5 " both_signs ideal model delta sigma weight residual False 2.55 1.16 1.39 2.00e-01 2.50e+01 4.86e+01 chirality pdb=" CB THR I 56 " pdb=" CA THR I 56 " pdb=" OG1 THR I 56 " pdb=" CG2 THR I 56 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.39 2.00e-01 2.50e+01 4.80e+01 ... (remaining 7623 not shown) Planarity restraints: 14817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY X 105 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO X 106 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO X 106 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO X 106 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 97 " 0.172 9.50e-02 1.11e+02 5.74e-02 3.53e+00 pdb=" NE ARG J 97 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG J 97 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG J 97 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 97 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG J 97 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG J 97 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG J 97 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG J 97 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 105 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO J 106 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO J 106 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 106 " 0.026 5.00e-02 4.00e+02 ... (remaining 14814 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 2549 2.13 - 2.75: 187970 2.75 - 3.36: 290184 3.36 - 3.98: 394848 3.98 - 4.60: 617938 Nonbonded interactions: 1493489 Sorted by model distance: nonbonded pdb=" OE2 GLU R 101 " pdb="HH22 ARG Z 197 " model vdw 1.512 1.850 nonbonded pdb=" OE2 GLU D 101 " pdb="HH22 ARG L 197 " model vdw 1.523 1.850 nonbonded pdb=" HE ARG M 28 " pdb=" OD2 ASP M 200 " model vdw 1.549 1.850 nonbonded pdb=" HE ARG 1 28 " pdb=" OD2 ASP 1 200 " model vdw 1.549 1.850 nonbonded pdb=" OD1 ASN Q 152 " pdb=" HG SER Q 154 " model vdw 1.566 1.850 ... (remaining 1493484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = (chain 'M' and (resid 1 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 96 through 222)) } ncs_group { reference = chain '2' selection = chain 'N' } ncs_group { reference = (chain 'A' and resid 11 through 250) selection = chain 'O' } ncs_group { reference = (chain 'B' and resid 5 through 250) selection = chain 'P' } ncs_group { reference = chain 'C' selection = (chain 'Q' and (resid 3 through 218 or resid 222 through 244)) } ncs_group { reference = (chain 'D' and (resid 3 through 52 or resid 55 through 243)) selection = chain 'R' } ncs_group { reference = chain 'E' selection = (chain 'S' and (resid 9 through 125 or resid 133 through 250)) } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = (chain 'G' and resid 5 through 247) selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = (chain 'J' and resid 2 through 204) selection = chain 'X' } ncs_group { reference = chain 'K' selection = (chain 'Y' and (resid 1 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 41 through 194)) } ncs_group { reference = chain 'L' selection = chain 'Z' } 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.120 Extract box with map and model: 13.540 Check model and map are aligned: 1.120 Set scattering table: 0.740 Process input model: 254.670 Find NCS groups from input model: 4.690 Set up NCS constraints: 0.540 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:9.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 288.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.004 0.044 50040 Z= 0.276 Angle : 0.529 11.636 67682 Z= 0.296 Chirality : 0.056 1.488 7626 Planarity : 0.004 0.074 8731 Dihedral : 12.591 89.522 18412 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.02 % Allowed : 0.06 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.11), residues: 6245 helix: 1.20 (0.11), residues: 2319 sheet: 0.16 (0.13), residues: 1576 loop : 0.26 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP U 217 HIS 0.005 0.001 HIS 1 195 PHE 0.025 0.001 PHE H 8 TYR 0.028 0.001 TYR L 180 ARG 0.009 0.001 ARG K 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 549 time to evaluate : 6.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.7701 (pm20) cc_final: 0.7434 (pm20) REVERT: E 108 ASN cc_start: 0.7891 (m110) cc_final: 0.7638 (m-40) REVERT: G 206 ASN cc_start: 0.7289 (m-40) cc_final: 0.6997 (m-40) REVERT: H 89 ASN cc_start: 0.8134 (m110) cc_final: 0.7908 (m110) REVERT: K 48 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7256 (mt-10) REVERT: L 228 ASP cc_start: 0.7811 (m-30) cc_final: 0.7497 (m-30) REVERT: M 62 ASP cc_start: 0.7155 (m-30) cc_final: 0.6918 (m-30) REVERT: M 119 LYS cc_start: 0.7073 (tttm) cc_final: 0.6540 (tttm) REVERT: S 108 ASN cc_start: 0.7933 (m110) cc_final: 0.7699 (m-40) REVERT: T 188 GLU cc_start: 0.7548 (tp30) cc_final: 0.6959 (tp30) REVERT: U 206 ASN cc_start: 0.7315 (m-40) cc_final: 0.7019 (m-40) REVERT: V 4 MET cc_start: 0.8568 (ttt) cc_final: 0.8256 (ttt) REVERT: Z 228 ASP cc_start: 0.7797 (m-30) cc_final: 0.7475 (m-30) REVERT: 1 62 ASP cc_start: 0.7152 (m-30) cc_final: 0.6918 (m-30) REVERT: 2 193 ARG cc_start: 0.8017 (ttt90) cc_final: 0.7561 (ttt90) REVERT: 2 217 MET cc_start: 0.8474 (mtp) cc_final: 0.7983 (mtp) outliers start: 1 outliers final: 2 residues processed: 550 average time/residue: 3.2586 time to fit residues: 2215.8464 Evaluate side-chains 357 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 355 time to evaluate : 6.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain T residue 5 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 1.9990 chunk 471 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 318 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 487 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 296 optimal weight: 0.0870 chunk 362 optimal weight: 3.9990 chunk 564 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN D 231 GLN F 60 GLN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN G 236 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 GLN I 91 GLN I 219 ASN N 125 GLN R 231 GLN T 31 GLN T 60 GLN ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 100 ASN ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 69 GLN W 91 GLN W 160 GLN W 194 ASN W 219 ASN X 112 ASN ** Z 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 125 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 50040 Z= 0.280 Angle : 0.554 11.637 67682 Z= 0.304 Chirality : 0.057 1.453 7626 Planarity : 0.004 0.062 8731 Dihedral : 4.773 23.710 6881 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.77 % Allowed : 5.59 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 6245 helix: 1.63 (0.10), residues: 2348 sheet: 0.02 (0.13), residues: 1521 loop : 0.12 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 217 HIS 0.006 0.001 HIS P 94 PHE 0.020 0.001 PHE F 179 TYR 0.018 0.001 TYR X 68 ARG 0.006 0.000 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 388 time to evaluate : 6.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.7709 (pm20) cc_final: 0.7450 (pm20) REVERT: E 108 ASN cc_start: 0.7910 (m110) cc_final: 0.7649 (m-40) REVERT: E 122 ARG cc_start: 0.7597 (ptp-110) cc_final: 0.7321 (mtm-85) REVERT: E 166 ARG cc_start: 0.8228 (ttt-90) cc_final: 0.7959 (ttt180) REVERT: G 206 ASN cc_start: 0.7370 (m-40) cc_final: 0.7104 (m-40) REVERT: I 89 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7928 (ttpt) REVERT: I 174 ASP cc_start: 0.8010 (m-30) cc_final: 0.7785 (m-30) REVERT: K 48 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7161 (mt-10) REVERT: L 228 ASP cc_start: 0.7806 (m-30) cc_final: 0.7534 (m-30) REVERT: S 108 ASN cc_start: 0.7909 (m110) cc_final: 0.7653 (m-40) REVERT: S 166 ARG cc_start: 0.8244 (ttt-90) cc_final: 0.8014 (ttt-90) REVERT: T 188 GLU cc_start: 0.7324 (tp30) cc_final: 0.6707 (tp30) REVERT: U 206 ASN cc_start: 0.7365 (m-40) cc_final: 0.7096 (m-40) REVERT: W 89 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7919 (ttpt) REVERT: W 174 ASP cc_start: 0.8020 (m-30) cc_final: 0.7744 (m-30) REVERT: Y 48 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6896 (mt-10) REVERT: Y 119 ASP cc_start: 0.8085 (p0) cc_final: 0.7856 (p0) REVERT: Z 143 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: Z 228 ASP cc_start: 0.7807 (m-30) cc_final: 0.7524 (m-30) outliers start: 41 outliers final: 15 residues processed: 417 average time/residue: 2.9218 time to fit residues: 1542.2085 Evaluate side-chains 382 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 365 time to evaluate : 6.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain W residue 22 GLN Chi-restraints excluded: chain W residue 73 GLU Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain 1 residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 470 optimal weight: 4.9990 chunk 384 optimal weight: 3.9990 chunk 155 optimal weight: 0.1980 chunk 565 optimal weight: 4.9990 chunk 611 optimal weight: 1.9990 chunk 503 optimal weight: 3.9990 chunk 561 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 453 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 GLN F 60 GLN F 100 ASN I 219 ASN N 125 GLN Q 59 GLN R 231 GLN S 99 HIS T 60 GLN U 236 GLN W 91 GLN W 219 ASN 2 125 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 50040 Z= 0.301 Angle : 0.530 11.562 67682 Z= 0.289 Chirality : 0.057 1.446 7626 Planarity : 0.004 0.068 8731 Dihedral : 4.758 26.551 6881 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.93 % Allowed : 6.74 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.10), residues: 6245 helix: 1.88 (0.11), residues: 2340 sheet: -0.13 (0.12), residues: 1556 loop : 0.15 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 199 HIS 0.007 0.001 HIS B 94 PHE 0.019 0.001 PHE F 179 TYR 0.015 0.001 TYR J 68 ARG 0.007 0.000 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 378 time to evaluate : 6.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 72 ARG cc_start: 0.8072 (mmp-170) cc_final: 0.7536 (mtp-110) REVERT: E 108 ASN cc_start: 0.7904 (m110) cc_final: 0.7626 (m-40) REVERT: E 225 GLN cc_start: 0.8393 (pm20) cc_final: 0.8076 (pm20) REVERT: G 206 ASN cc_start: 0.7287 (m-40) cc_final: 0.7041 (m-40) REVERT: I 89 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7936 (ttpt) REVERT: L 228 ASP cc_start: 0.7762 (m-30) cc_final: 0.7483 (m-30) REVERT: O 216 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8648 (t) REVERT: S 72 ARG cc_start: 0.8088 (mmp-170) cc_final: 0.7548 (mtp-110) REVERT: S 108 ASN cc_start: 0.7915 (m110) cc_final: 0.7639 (m-40) REVERT: S 225 GLN cc_start: 0.8332 (pm20) cc_final: 0.8061 (pm20) REVERT: T 188 GLU cc_start: 0.7359 (tp30) cc_final: 0.6695 (tp30) REVERT: U 206 ASN cc_start: 0.7274 (m-40) cc_final: 0.7027 (m-40) REVERT: Y 48 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6795 (mt-10) REVERT: Z 143 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: Z 228 ASP cc_start: 0.7764 (m-30) cc_final: 0.7490 (m-30) REVERT: 1 109 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8293 (m) REVERT: 1 126 ASP cc_start: 0.7578 (t70) cc_final: 0.7249 (t0) outliers start: 49 outliers final: 20 residues processed: 410 average time/residue: 2.8164 time to fit residues: 1478.9229 Evaluate side-chains 379 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 355 time to evaluate : 6.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain J residue 65 MET Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain N residue 125 GLN Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain W residue 73 GLU Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain 1 residue 109 THR Chi-restraints excluded: chain 2 residue 125 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 2.9990 chunk 425 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 379 optimal weight: 10.0000 chunk 567 optimal weight: 3.9990 chunk 601 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 538 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN F 60 GLN F 100 ASN I 91 GLN I 219 ASN P 241 GLN Q 59 GLN R 231 GLN T 60 GLN ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 219 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 50040 Z= 0.334 Angle : 0.533 11.516 67682 Z= 0.290 Chirality : 0.057 1.430 7626 Planarity : 0.004 0.063 8731 Dihedral : 4.777 28.294 6881 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 7.52 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.10), residues: 6245 helix: 1.89 (0.11), residues: 2338 sheet: -0.21 (0.12), residues: 1541 loop : 0.10 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 199 HIS 0.006 0.001 HIS B 94 PHE 0.017 0.001 PHE F 179 TYR 0.015 0.001 TYR X 68 ARG 0.006 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 361 time to evaluate : 6.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 72 ARG cc_start: 0.8160 (mmp-170) cc_final: 0.7533 (mtp-110) REVERT: E 108 ASN cc_start: 0.7945 (m110) cc_final: 0.7655 (m-40) REVERT: E 225 GLN cc_start: 0.8379 (pm20) cc_final: 0.8096 (pm20) REVERT: E 232 ASP cc_start: 0.7112 (p0) cc_final: 0.6823 (p0) REVERT: G 206 ASN cc_start: 0.7289 (m-40) cc_final: 0.7041 (m-40) REVERT: I 89 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7906 (ttpt) REVERT: L 228 ASP cc_start: 0.7755 (m-30) cc_final: 0.7474 (m-30) REVERT: O 216 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8477 (p) REVERT: S 72 ARG cc_start: 0.8158 (mmp-170) cc_final: 0.7523 (mtp-110) REVERT: S 108 ASN cc_start: 0.7913 (m110) cc_final: 0.7636 (m-40) REVERT: S 225 GLN cc_start: 0.8351 (pm20) cc_final: 0.8097 (pm20) REVERT: S 232 ASP cc_start: 0.7115 (p0) cc_final: 0.6828 (p0) REVERT: U 97 SER cc_start: 0.8815 (t) cc_final: 0.8514 (p) REVERT: U 206 ASN cc_start: 0.7286 (m-40) cc_final: 0.7036 (m-40) REVERT: Y 48 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6792 (mt-10) REVERT: Z 143 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: Z 228 ASP cc_start: 0.7753 (m-30) cc_final: 0.7479 (m-30) REVERT: 1 109 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8300 (m) REVERT: 1 126 ASP cc_start: 0.7582 (t70) cc_final: 0.7218 (t0) outliers start: 57 outliers final: 25 residues processed: 397 average time/residue: 2.8463 time to fit residues: 1444.1005 Evaluate side-chains 380 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 351 time to evaluate : 6.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 194 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 231 GLN Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain W residue 73 GLU Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain 1 residue 109 THR Chi-restraints excluded: chain 1 residue 134 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 3.9990 chunk 341 optimal weight: 0.0040 chunk 8 optimal weight: 2.9990 chunk 447 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 513 optimal weight: 0.2980 chunk 415 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 539 optimal weight: 2.9990 chunk 151 optimal weight: 0.0060 overall best weight: 0.8612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN F 60 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN I 219 ASN P 241 GLN Q 59 GLN R 231 GLN T 31 GLN T 60 GLN ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 219 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 50040 Z= 0.174 Angle : 0.488 11.530 67682 Z= 0.266 Chirality : 0.056 1.430 7626 Planarity : 0.004 0.059 8731 Dihedral : 4.561 23.847 6881 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.70 % Allowed : 8.05 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.11), residues: 6245 helix: 2.16 (0.11), residues: 2334 sheet: -0.17 (0.12), residues: 1536 loop : 0.21 (0.13), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 199 HIS 0.004 0.001 HIS P 94 PHE 0.016 0.001 PHE F 179 TYR 0.015 0.001 TYR X 68 ARG 0.004 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 378 time to evaluate : 6.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 72 ARG cc_start: 0.8089 (mmp-170) cc_final: 0.7505 (mtp-110) REVERT: E 108 ASN cc_start: 0.7998 (m110) cc_final: 0.7662 (m110) REVERT: E 225 GLN cc_start: 0.8379 (pm20) cc_final: 0.8091 (pm20) REVERT: E 232 ASP cc_start: 0.7047 (p0) cc_final: 0.6796 (p0) REVERT: G 97 SER cc_start: 0.8771 (t) cc_final: 0.8511 (p) REVERT: I 89 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8080 (ttpp) REVERT: L 228 ASP cc_start: 0.7718 (m-30) cc_final: 0.7441 (m-30) REVERT: O 216 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8480 (p) REVERT: R 144 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7416 (tt0) REVERT: S 72 ARG cc_start: 0.8141 (mmp-170) cc_final: 0.7511 (mtp-110) REVERT: S 108 ASN cc_start: 0.7995 (m110) cc_final: 0.7668 (m110) REVERT: S 225 GLN cc_start: 0.8332 (pm20) cc_final: 0.8079 (pm20) REVERT: S 232 ASP cc_start: 0.7055 (p0) cc_final: 0.6783 (p0) REVERT: U 97 SER cc_start: 0.8769 (t) cc_final: 0.8515 (p) REVERT: Y 48 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6804 (mt-10) REVERT: Z 228 ASP cc_start: 0.7713 (m-30) cc_final: 0.7431 (m-30) REVERT: 1 126 ASP cc_start: 0.7569 (t70) cc_final: 0.7168 (t0) outliers start: 37 outliers final: 17 residues processed: 402 average time/residue: 2.8303 time to fit residues: 1454.6745 Evaluate side-chains 373 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 354 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 194 LEU Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain W residue 73 GLU Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain 1 residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 0.9990 chunk 541 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 352 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 601 optimal weight: 2.9990 chunk 499 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN C 59 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN F 60 GLN I 91 GLN I 219 ASN N 213 GLN Q 59 GLN T 31 GLN T 60 GLN ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 219 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 50040 Z= 0.205 Angle : 0.486 11.445 67682 Z= 0.263 Chirality : 0.056 1.414 7626 Planarity : 0.004 0.061 8731 Dihedral : 4.494 22.887 6881 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.85 % Allowed : 8.41 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.11), residues: 6245 helix: 2.34 (0.11), residues: 2336 sheet: -0.17 (0.12), residues: 1545 loop : 0.21 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 199 HIS 0.004 0.001 HIS B 94 PHE 0.016 0.001 PHE T 179 TYR 0.014 0.001 TYR X 68 ARG 0.005 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 368 time to evaluate : 7.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 72 ARG cc_start: 0.8162 (mmp-170) cc_final: 0.7501 (mtp-110) REVERT: E 108 ASN cc_start: 0.7991 (m110) cc_final: 0.7657 (m110) REVERT: E 225 GLN cc_start: 0.8390 (pm20) cc_final: 0.8103 (pm20) REVERT: E 232 ASP cc_start: 0.6986 (p0) cc_final: 0.6732 (p0) REVERT: G 97 SER cc_start: 0.8771 (t) cc_final: 0.8506 (p) REVERT: G 233 ASP cc_start: 0.7319 (t0) cc_final: 0.7073 (t0) REVERT: I 89 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8089 (ttpp) REVERT: L 228 ASP cc_start: 0.7713 (m-30) cc_final: 0.7437 (m-30) REVERT: O 216 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8379 (p) REVERT: S 20 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7616 (mtm-85) REVERT: S 72 ARG cc_start: 0.8157 (mmp-170) cc_final: 0.7496 (mtp-110) REVERT: S 108 ASN cc_start: 0.7985 (m110) cc_final: 0.7660 (m110) REVERT: S 225 GLN cc_start: 0.8340 (pm20) cc_final: 0.8082 (pm20) REVERT: S 232 ASP cc_start: 0.7007 (p0) cc_final: 0.6770 (p0) REVERT: U 97 SER cc_start: 0.8772 (t) cc_final: 0.8517 (p) REVERT: U 233 ASP cc_start: 0.7371 (t0) cc_final: 0.7102 (t0) REVERT: V 159 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8240 (mp) REVERT: Y 48 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: Z 228 ASP cc_start: 0.7731 (m-30) cc_final: 0.7465 (m-30) outliers start: 45 outliers final: 24 residues processed: 399 average time/residue: 2.7810 time to fit residues: 1429.8836 Evaluate side-chains 377 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 350 time to evaluate : 6.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 194 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain W residue 73 GLU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 439 optimal weight: 2.9990 chunk 340 optimal weight: 0.7980 chunk 506 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 599 optimal weight: 4.9990 chunk 375 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN F 31 GLN F 60 GLN I 91 GLN I 219 ASN Q 59 GLN ** R 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 GLN T 60 GLN ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 219 ASN 2 213 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 50040 Z= 0.292 Angle : 0.510 11.442 67682 Z= 0.276 Chirality : 0.056 1.413 7626 Planarity : 0.004 0.079 8731 Dihedral : 4.581 24.263 6881 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.06 % Allowed : 8.77 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.11), residues: 6245 helix: 2.26 (0.11), residues: 2342 sheet: -0.23 (0.12), residues: 1551 loop : 0.16 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 199 HIS 0.005 0.001 HIS P 94 PHE 0.016 0.001 PHE F 179 TYR 0.015 0.001 TYR X 68 ARG 0.011 0.000 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 359 time to evaluate : 6.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.6967 (mp-120) REVERT: D 144 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: E 72 ARG cc_start: 0.8176 (mmp-170) cc_final: 0.7511 (mtp-110) REVERT: E 108 ASN cc_start: 0.8038 (m110) cc_final: 0.7695 (m110) REVERT: E 225 GLN cc_start: 0.8392 (pm20) cc_final: 0.8096 (pm20) REVERT: E 232 ASP cc_start: 0.6986 (p0) cc_final: 0.6674 (p0) REVERT: G 97 SER cc_start: 0.8790 (t) cc_final: 0.8486 (p) REVERT: I 89 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7885 (ttpt) REVERT: K 98 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8152 (mm-40) REVERT: L 228 ASP cc_start: 0.7765 (m-30) cc_final: 0.7492 (m-30) REVERT: O 216 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8374 (p) REVERT: R 144 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: S 20 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7621 (mtm-85) REVERT: S 72 ARG cc_start: 0.8169 (mmp-170) cc_final: 0.7504 (mtp-110) REVERT: S 108 ASN cc_start: 0.8033 (m110) cc_final: 0.7695 (m110) REVERT: S 225 GLN cc_start: 0.8332 (pm20) cc_final: 0.8022 (pm20) REVERT: S 232 ASP cc_start: 0.6981 (p0) cc_final: 0.6713 (p0) REVERT: U 97 SER cc_start: 0.8790 (t) cc_final: 0.8495 (p) REVERT: V 159 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8249 (mp) REVERT: Y 48 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: Y 98 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8057 (mm-40) REVERT: Z 228 ASP cc_start: 0.7747 (m-30) cc_final: 0.7480 (m-30) REVERT: 1 126 ASP cc_start: 0.7599 (t70) cc_final: 0.7283 (t0) outliers start: 56 outliers final: 28 residues processed: 396 average time/residue: 2.7788 time to fit residues: 1415.0577 Evaluate side-chains 374 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 340 time to evaluate : 6.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 194 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 63 LYS Chi-restraints excluded: chain R residue 144 GLU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 381 optimal weight: 2.9990 chunk 408 optimal weight: 3.9990 chunk 296 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 471 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN F 60 GLN I 22 GLN I 219 ASN Q 59 GLN R 231 GLN T 60 GLN ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 219 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 50040 Z= 0.338 Angle : 0.522 11.442 67682 Z= 0.283 Chirality : 0.057 1.409 7626 Planarity : 0.004 0.062 8731 Dihedral : 4.632 25.485 6881 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.98 % Allowed : 9.11 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.11), residues: 6245 helix: 2.20 (0.11), residues: 2342 sheet: -0.23 (0.12), residues: 1547 loop : 0.12 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 199 HIS 0.005 0.001 HIS B 94 PHE 0.016 0.001 PHE F 179 TYR 0.014 0.001 TYR X 68 ARG 0.008 0.000 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 341 time to evaluate : 6.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 144 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: E 72 ARG cc_start: 0.8183 (mmp-170) cc_final: 0.7518 (mtp-110) REVERT: E 108 ASN cc_start: 0.8045 (m110) cc_final: 0.7696 (m-40) REVERT: E 225 GLN cc_start: 0.8392 (pm20) cc_final: 0.8099 (pm20) REVERT: E 232 ASP cc_start: 0.6984 (p0) cc_final: 0.6691 (p0) REVERT: G 97 SER cc_start: 0.8794 (t) cc_final: 0.8488 (p) REVERT: I 89 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7888 (ttpt) REVERT: K 98 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8135 (mm-40) REVERT: L 228 ASP cc_start: 0.7771 (m-30) cc_final: 0.7496 (m-30) REVERT: O 216 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8313 (p) REVERT: R 144 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: S 72 ARG cc_start: 0.8176 (mmp-170) cc_final: 0.7508 (mtp-110) REVERT: S 108 ASN cc_start: 0.8037 (m110) cc_final: 0.7696 (m-40) REVERT: S 225 GLN cc_start: 0.8333 (pm20) cc_final: 0.8079 (pm20) REVERT: S 232 ASP cc_start: 0.6980 (p0) cc_final: 0.6688 (p0) REVERT: U 97 SER cc_start: 0.8794 (t) cc_final: 0.8490 (p) REVERT: U 206 ASN cc_start: 0.7289 (m-40) cc_final: 0.7047 (m-40) REVERT: V 159 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8271 (mp) REVERT: Y 48 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6666 (mt-10) REVERT: Z 228 ASP cc_start: 0.7752 (m-30) cc_final: 0.7484 (m-30) REVERT: 1 126 ASP cc_start: 0.7610 (t70) cc_final: 0.7258 (t0) outliers start: 52 outliers final: 31 residues processed: 376 average time/residue: 2.7930 time to fit residues: 1354.3204 Evaluate side-chains 373 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 337 time to evaluate : 6.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 194 LEU Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 63 LYS Chi-restraints excluded: chain R residue 144 GLU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain X residue 113 SER Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 1.9990 chunk 574 optimal weight: 2.9990 chunk 524 optimal weight: 0.9990 chunk 558 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 438 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 504 optimal weight: 2.9990 chunk 528 optimal weight: 0.6980 chunk 556 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN C 59 GLN F 31 GLN F 60 GLN I 22 GLN I 91 GLN I 219 ASN Q 59 GLN T 60 GLN ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 GLN W 91 GLN W 219 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 50040 Z= 0.261 Angle : 0.503 11.479 67682 Z= 0.273 Chirality : 0.056 1.417 7626 Planarity : 0.004 0.060 8731 Dihedral : 4.577 25.542 6881 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.89 % Allowed : 9.26 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.11), residues: 6245 helix: 2.28 (0.11), residues: 2342 sheet: -0.22 (0.12), residues: 1559 loop : 0.17 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 199 HIS 0.004 0.001 HIS O 209 PHE 0.015 0.001 PHE F 179 TYR 0.015 0.001 TYR X 68 ARG 0.006 0.000 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 344 time to evaluate : 6.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 144 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: E 72 ARG cc_start: 0.8179 (mmp-170) cc_final: 0.7512 (mtp-110) REVERT: E 108 ASN cc_start: 0.8026 (m110) cc_final: 0.7670 (m110) REVERT: E 225 GLN cc_start: 0.8393 (pm20) cc_final: 0.8094 (pm20) REVERT: E 232 ASP cc_start: 0.6961 (p0) cc_final: 0.6671 (p0) REVERT: F 188 GLU cc_start: 0.7469 (tp30) cc_final: 0.7250 (tp30) REVERT: G 97 SER cc_start: 0.8787 (t) cc_final: 0.8484 (p) REVERT: L 228 ASP cc_start: 0.7753 (m-30) cc_final: 0.7481 (m-30) REVERT: O 216 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8315 (t) REVERT: S 72 ARG cc_start: 0.8175 (mmp-170) cc_final: 0.7504 (mtp-110) REVERT: S 108 ASN cc_start: 0.8018 (m110) cc_final: 0.7667 (m110) REVERT: S 225 GLN cc_start: 0.8333 (pm20) cc_final: 0.8033 (pm20) REVERT: S 232 ASP cc_start: 0.6957 (p0) cc_final: 0.6690 (p0) REVERT: U 97 SER cc_start: 0.8785 (t) cc_final: 0.8487 (p) REVERT: V 159 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8259 (mp) REVERT: Y 48 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: Z 228 ASP cc_start: 0.7729 (m-30) cc_final: 0.7464 (m-30) REVERT: 1 126 ASP cc_start: 0.7569 (t70) cc_final: 0.7225 (t0) outliers start: 47 outliers final: 26 residues processed: 378 average time/residue: 2.7892 time to fit residues: 1362.4210 Evaluate side-chains 362 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 332 time to evaluate : 6.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 63 LYS Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain W residue 174 ASP Chi-restraints excluded: chain X residue 113 SER Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain 1 residue 134 GLU Chi-restraints excluded: chain 1 residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 2.9990 chunk 590 optimal weight: 5.9990 chunk 360 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 410 optimal weight: 0.9990 chunk 619 optimal weight: 0.8980 chunk 570 optimal weight: 1.9990 chunk 493 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 381 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 177 GLN F 31 GLN F 60 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN I 91 GLN I 219 ASN Q 59 GLN T 60 GLN ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 219 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50040 Z= 0.189 Angle : 0.480 11.456 67682 Z= 0.260 Chirality : 0.056 1.417 7626 Planarity : 0.004 0.059 8731 Dihedral : 4.453 24.193 6881 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.62 % Allowed : 9.62 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.11), residues: 6245 helix: 2.43 (0.11), residues: 2348 sheet: -0.13 (0.12), residues: 1537 loop : 0.18 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 199 HIS 0.006 0.001 HIS 1 108 PHE 0.015 0.001 PHE F 179 TYR 0.015 0.001 TYR X 68 ARG 0.006 0.000 ARG X 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12490 Ramachandran restraints generated. 6245 Oldfield, 0 Emsley, 6245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 368 time to evaluate : 6.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 20 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7651 (mtm-85) REVERT: E 72 ARG cc_start: 0.8173 (mmp-170) cc_final: 0.7504 (mtp-110) REVERT: E 108 ASN cc_start: 0.8020 (m110) cc_final: 0.7653 (m110) REVERT: E 225 GLN cc_start: 0.8395 (pm20) cc_final: 0.8091 (pm20) REVERT: E 232 ASP cc_start: 0.6961 (p0) cc_final: 0.6720 (p0) REVERT: F 188 GLU cc_start: 0.7457 (tp30) cc_final: 0.7244 (tp30) REVERT: G 97 SER cc_start: 0.8767 (t) cc_final: 0.8493 (p) REVERT: L 228 ASP cc_start: 0.7721 (m-30) cc_final: 0.7453 (m-30) REVERT: R 144 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: R 218 ASP cc_start: 0.7662 (m-30) cc_final: 0.7457 (p0) REVERT: S 72 ARG cc_start: 0.8169 (mmp-170) cc_final: 0.7496 (mtp-110) REVERT: S 108 ASN cc_start: 0.8013 (m110) cc_final: 0.7649 (m110) REVERT: S 225 GLN cc_start: 0.8332 (pm20) cc_final: 0.8020 (pm20) REVERT: S 232 ASP cc_start: 0.6965 (p0) cc_final: 0.6732 (p0) REVERT: U 97 SER cc_start: 0.8764 (t) cc_final: 0.8495 (p) REVERT: V 159 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8276 (mp) REVERT: Y 48 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: Z 228 ASP cc_start: 0.7692 (m-30) cc_final: 0.7439 (m-30) REVERT: 1 126 ASP cc_start: 0.7555 (t70) cc_final: 0.7187 (t0) outliers start: 33 outliers final: 23 residues processed: 390 average time/residue: 2.6900 time to fit residues: 1365.2706 Evaluate side-chains 368 residues out of total 5293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 342 time to evaluate : 6.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 5 ASN Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain R residue 63 LYS Chi-restraints excluded: chain R residue 144 GLU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 159 LEU Chi-restraints excluded: chain Y residue 48 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 2.9990 chunk 525 optimal weight: 1.9990 chunk 151 optimal weight: 0.4980 chunk 454 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 494 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 507 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN F 31 GLN F 60 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN I 219 ASN P 241 GLN Q 59 GLN T 31 GLN T 60 GLN ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 219 ASN 1 95 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.084976 restraints weight = 191476.455| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.07 r_work: 0.2956 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 50040 Z= 0.258 Angle : 0.498 11.424 67682 Z= 0.269 Chirality : 0.056 1.412 7626 Planarity : 0.004 0.062 8731 Dihedral : 4.501 24.571 6881 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.66 % Allowed : 9.81 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.11), residues: 6245 helix: 2.38 (0.11), residues: 2354 sheet: -0.19 (0.12), residues: 1561 loop : 0.19 (0.13), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 199 HIS 0.004 0.001 HIS O 209 PHE 0.015 0.001 PHE F 179 TYR 0.014 0.001 TYR X 68 ARG 0.006 0.000 ARG X 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24127.04 seconds wall clock time: 418 minutes 9.79 seconds (25089.79 seconds total)