Starting phenix.real_space_refine on Sat Mar 16 02:40:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhg_22336/03_2024/7jhg_22336_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhg_22336/03_2024/7jhg_22336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhg_22336/03_2024/7jhg_22336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhg_22336/03_2024/7jhg_22336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhg_22336/03_2024/7jhg_22336_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhg_22336/03_2024/7jhg_22336_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 6 5.49 5 S 51 5.16 5 C 8589 2.51 5 N 2260 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G ARG 299": "NH1" <-> "NH2" Residue "M TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13457 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3083 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 736 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 11, 'TRANS': 81} Chain: "G" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2421 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "M" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain: "L" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'TAK': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 6.15, per 1000 atoms: 0.46 Number of scatterers: 13457 At special positions: 0 Unit cell: (100.842, 129.654, 164.64, 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 51 16.00 P 6 15.00 O 2551 8.00 N 2260 7.00 C 8589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 212 " distance=2.03 Simple disulfide: pdb=" SG CYS N 31 " - pdb=" SG CYS N 105 " distance=2.04 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 Links applied ALPHA1-4 " GLC D 1 " - " GLC D 2 " Time building additional restraints: 4.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 22 sheets defined 25.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 77.74 Creating SS restraints... Processing helix chain 'A' and resid 60 through 72 removed outlier: 4.203A pdb=" N LYS A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 115 through 134 removed outlier: 3.545A pdb=" N ARG A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.792A pdb=" N MET A 165 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 168 " --> pdb=" O MET A 165 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 169 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.937A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 408 through 421 removed outlier: 3.786A pdb=" N MET A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 548 removed outlier: 3.606A pdb=" N CYS A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.895A pdb=" N GLN B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 215 " --> pdb=" O HIS B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 210 through 215' Processing helix chain 'G' and resid 27 through 35 removed outlier: 3.698A pdb=" N SER G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 41 Processing helix chain 'G' and resid 57 through 67 removed outlier: 3.905A pdb=" N PHE G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 97 Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 114 through 121 removed outlier: 3.595A pdb=" N GLU G 119 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 147 removed outlier: 3.595A pdb=" N ARG G 147 " --> pdb=" O SER G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 177 Processing helix chain 'G' and resid 193 through 196 No H-bonds generated for 'chain 'G' and resid 193 through 196' Processing helix chain 'G' and resid 213 through 222 Processing helix chain 'G' and resid 243 through 251 removed outlier: 3.544A pdb=" N ILE G 247 " --> pdb=" O PHE G 244 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 248 " --> pdb=" O ASP G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 266 Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.624A pdb=" N GLU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 323 removed outlier: 3.683A pdb=" N GLN G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 31 removed outlier: 3.638A pdb=" N ASP M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 51 Proline residue: M 48 - end of helix Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 91 through 97 removed outlier: 3.815A pdb=" N VAL M 97 " --> pdb=" O THR M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 142 removed outlier: 3.753A pdb=" N GLU M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA M 141 " --> pdb=" O LYS M 137 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS M 142 " --> pdb=" O GLU M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 164 Proline residue: M 159 - end of helix removed outlier: 5.047A pdb=" N ASP M 164 " --> pdb=" O LEU M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 200 removed outlier: 3.690A pdb=" N ILE M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'M' and resid 229 through 238 removed outlier: 4.136A pdb=" N SER M 233 " --> pdb=" O TRP M 230 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR M 237 " --> pdb=" O ASN M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 283 Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.881A pdb=" N GLU M 291 " --> pdb=" O ASP M 287 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA M 292 " --> pdb=" O GLU M 288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL M 293 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 313 removed outlier: 3.894A pdb=" N GLU M 310 " --> pdb=" O SER M 306 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LYS M 313 " --> pdb=" O GLU M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 325 Processing helix chain 'M' and resid 334 through 351 removed outlier: 4.039A pdb=" N TRP M 340 " --> pdb=" O SER M 337 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR M 341 " --> pdb=" O ALA M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 357 through 366 Processing helix chain 'L' and resid 124 through 127 No H-bonds generated for 'chain 'L' and resid 124 through 127' Processing helix chain 'L' and resid 151 through 153 No H-bonds generated for 'chain 'L' and resid 151 through 153' Processing helix chain 'L' and resid 185 through 187 No H-bonds generated for 'chain 'L' and resid 185 through 187' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 Processing sheet with id= B, first strand: chain 'A' and resid 402 through 404 removed outlier: 3.530A pdb=" N LYS A 427 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 23 through 26 removed outlier: 7.205A pdb=" N VAL A 32 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 250 through 255 removed outlier: 3.574A pdb=" N LYS B 270 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 255 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 50 through 52 removed outlier: 7.668A pdb=" N PHE G 51 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY G 84 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP G 76 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE G 82 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 278 through 280 removed outlier: 8.283A pdb=" N CYS G 279 " --> pdb=" O ARG G 299 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL G 301 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY G 311 " --> pdb=" O VAL G 302 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 7 through 10 Processing sheet with id= H, first strand: chain 'M' and resid 59 through 63 removed outlier: 6.023A pdb=" N ALA M 264 " --> pdb=" O PRO M 107 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE M 266 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA M 105 " --> pdb=" O ILE M 266 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 224 through 227 removed outlier: 3.996A pdb=" N ASN M 227 " --> pdb=" O SER M 114 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER M 114 " --> pdb=" O ASN M 227 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 12 through 14 removed outlier: 4.133A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.510A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.899A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.143A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA L 131 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 145 through 149 removed outlier: 3.662A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL L 197 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL L 206 " --> pdb=" O VAL L 197 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.518A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER H 10 " --> pdb=" O SER H 24 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.507A pdb=" N ALA H 95 " --> pdb=" O VAL H 125 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.665A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.826A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 136 through 140 removed outlier: 4.561A pdb=" N GLY H 155 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.735A pdb=" N TYR H 210 " --> pdb=" O VAL H 227 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 14 through 17 removed outlier: 3.572A pdb=" N CYS N 31 " --> pdb=" O VAL N 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'N' and resid 123 through 126 removed outlier: 3.522A pdb=" N VAL N 126 " --> pdb=" O ALA N 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL N 102 " --> pdb=" O GLN N 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER N 44 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ARG N 47 " --> pdb=" O PHE N 56 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE N 56 " --> pdb=" O ARG N 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE N 68 " --> pdb=" O VAL N 59 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 957 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: 4.34 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4259 1.34 - 1.46: 3233 1.46 - 1.58: 6199 1.58 - 1.70: 9 1.70 - 1.82: 81 Bond restraints: 13781 Sorted by residual: bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.76e+01 bond pdb=" C5 ATP G 401 " pdb=" C6 ATP G 401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" C8 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.29e+01 bond pdb=" C5 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.74e+01 bond pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.53e+01 ... (remaining 13776 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.78: 484 106.78 - 114.16: 7839 114.16 - 121.54: 6959 121.54 - 128.93: 3334 128.93 - 136.31: 100 Bond angle restraints: 18716 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 120.98 18.89 1.00e+00 1.00e+00 3.57e+02 angle pdb=" PA ATP G 401 " pdb=" O3A ATP G 401 " pdb=" PB ATP G 401 " ideal model delta sigma weight residual 136.83 121.49 15.34 1.00e+00 1.00e+00 2.35e+02 angle pdb=" C5 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 126.80 118.73 8.07 1.00e+00 1.00e+00 6.52e+01 angle pdb=" N3 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 127.04 134.99 -7.95 1.15e+00 7.59e-01 4.80e+01 angle pdb=" N1 ATP G 401 " pdb=" C2 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 128.69 123.67 5.02 1.00e+00 1.00e+00 2.52e+01 ... (remaining 18711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.79: 8173 27.79 - 55.57: 111 55.57 - 83.36: 14 83.36 - 111.15: 5 111.15 - 138.93: 3 Dihedral angle restraints: 8306 sinusoidal: 3345 harmonic: 4961 Sorted by residual: dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 21.16 71.84 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" C5' ADP G 402 " pdb=" O5' ADP G 402 " pdb=" PA ADP G 402 " pdb=" O2A ADP G 402 " ideal model delta sinusoidal sigma weight residual 300.00 161.07 138.93 1 2.00e+01 2.50e-03 4.21e+01 dihedral pdb=" C5' AMP G 403 " pdb=" O5' AMP G 403 " pdb=" P AMP G 403 " pdb=" O3P AMP G 403 " ideal model delta sinusoidal sigma weight residual -60.00 54.97 -114.97 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 8303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1864 0.081 - 0.162: 211 0.162 - 0.243: 10 0.243 - 0.325: 1 0.325 - 0.406: 1 Chirality restraints: 2087 Sorted by residual: chirality pdb=" C1 GLC D 2 " pdb=" O4 GLC D 1 " pdb=" C2 GLC D 2 " pdb=" O5 GLC D 2 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 8.21e+00 chirality pdb=" CB ILE G 106 " pdb=" CA ILE G 106 " pdb=" CG1 ILE G 106 " pdb=" CG2 ILE G 106 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.36 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 2084 not shown) Planarity restraints: 2363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.56e+00 pdb=" N PRO L 9 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 430 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO A 431 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 143 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO A 144 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.031 5.00e-02 4.00e+02 ... (remaining 2360 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1422 2.76 - 3.47: 17893 3.47 - 4.19: 31140 4.19 - 4.90: 53886 Nonbonded interactions: 104342 Sorted by model distance: nonbonded pdb=" N VAL A 13 " pdb=" C PHE M 371 " model vdw 1.330 3.350 nonbonded pdb=" N VAL A 13 " pdb=" O PHE M 371 " model vdw 2.253 2.520 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.318 2.440 nonbonded pdb=" O HIS A 220 " pdb=" OG1 THR A 223 " model vdw 2.326 2.440 nonbonded pdb=" OG1 THR G 89 " pdb=" O1B ADP G 402 " model vdw 2.329 2.440 ... (remaining 104337 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.070 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.600 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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 0.082 13781 Z= 0.230 Angle : 0.776 18.887 18716 Z= 0.437 Chirality : 0.050 0.406 2087 Planarity : 0.007 0.059 2363 Dihedral : 10.242 138.933 5107 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.07 % Allowed : 1.77 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.17), residues: 1683 helix: -2.89 (0.15), residues: 430 sheet: -1.67 (0.26), residues: 334 loop : -2.12 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 200 HIS 0.009 0.001 HIS B 257 PHE 0.029 0.002 PHE A 225 TYR 0.018 0.002 TYR H 102 ARG 0.010 0.000 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7927 (mmt180) cc_final: 0.7347 (mtm180) REVERT: A 117 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7492 (tp30) REVERT: A 141 ASP cc_start: 0.7325 (t0) cc_final: 0.6963 (m-30) REVERT: A 226 LYS cc_start: 0.8228 (tttt) cc_final: 0.7960 (tptp) REVERT: A 268 GLU cc_start: 0.8602 (tp30) cc_final: 0.7789 (pm20) REVERT: A 536 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7670 (mt-10) REVERT: B 204 SER cc_start: 0.6588 (m) cc_final: 0.6288 (p) REVERT: B 249 SER cc_start: 0.7198 (t) cc_final: 0.6839 (p) REVERT: B 251 MET cc_start: 0.7669 (ttm) cc_final: 0.7425 (ttt) REVERT: B 261 LYS cc_start: 0.8681 (tptt) cc_final: 0.8359 (mmtm) REVERT: G 30 THR cc_start: 0.8416 (m) cc_final: 0.8022 (p) REVERT: G 39 TYR cc_start: 0.7490 (t80) cc_final: 0.6745 (t80) REVERT: G 58 LYS cc_start: 0.8106 (tttt) cc_final: 0.7902 (tptm) REVERT: G 105 GLN cc_start: 0.7779 (mt0) cc_final: 0.7543 (tm-30) REVERT: G 119 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7625 (pt0) REVERT: G 189 MET cc_start: 0.7968 (mmt) cc_final: 0.7458 (mmp) REVERT: G 198 ILE cc_start: 0.8086 (mt) cc_final: 0.7752 (mm) REVERT: G 201 TYR cc_start: 0.6626 (m-80) cc_final: 0.5778 (m-80) REVERT: G 206 MET cc_start: 0.6808 (mtm) cc_final: 0.6432 (ttm) REVERT: G 240 ILE cc_start: 0.6535 (tt) cc_final: 0.5593 (tt) REVERT: G 264 LYS cc_start: 0.8493 (mttt) cc_final: 0.8255 (mtmt) REVERT: G 280 TYR cc_start: 0.7134 (m-80) cc_final: 0.6694 (m-10) REVERT: M 10 TRP cc_start: 0.6793 (m-10) cc_final: 0.6530 (m-10) REVERT: M 22 GLU cc_start: 0.6652 (mt-10) cc_final: 0.5860 (tm-30) REVERT: M 55 ASP cc_start: 0.5917 (p0) cc_final: 0.5532 (t70) REVERT: M 90 TYR cc_start: 0.6264 (m-80) cc_final: 0.5268 (m-80) REVERT: M 171 TYR cc_start: 0.7592 (t80) cc_final: 0.7039 (t80) REVERT: M 189 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8379 (mmtm) REVERT: M 203 HIS cc_start: 0.4667 (m90) cc_final: 0.4441 (m-70) REVERT: M 270 SER cc_start: 0.4901 (t) cc_final: 0.4429 (p) REVERT: M 313 LYS cc_start: 0.6910 (mttt) cc_final: 0.6683 (tppt) REVERT: M 332 ASN cc_start: 0.7701 (p0) cc_final: 0.7048 (t0) REVERT: M 355 GLN cc_start: 0.8654 (mt0) cc_final: 0.8228 (tt0) REVERT: M 356 THR cc_start: 0.8225 (p) cc_final: 0.7775 (t) REVERT: L 5 MET cc_start: 0.5736 (ptp) cc_final: 0.5454 (ptp) REVERT: L 25 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.7482 (mmm160) REVERT: L 71 ASP cc_start: 0.7756 (t70) cc_final: 0.7521 (t70) REVERT: L 80 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7683 (tp40) REVERT: L 101 GLN cc_start: 0.8452 (mm110) cc_final: 0.8099 (mm110) REVERT: L 143 ARG cc_start: 0.7960 (ttt-90) cc_final: 0.7309 (tpt90) REVERT: L 150 LYS cc_start: 0.8603 (mttt) cc_final: 0.8110 (mtmm) REVERT: L 191 LYS cc_start: 0.9083 (tttm) cc_final: 0.8532 (tptp) REVERT: L 196 GLU cc_start: 0.8387 (tt0) cc_final: 0.7488 (tp30) REVERT: H 163 PRO cc_start: 0.7586 (Cg_exo) cc_final: 0.7128 (Cg_endo) REVERT: H 164 GLU cc_start: 0.7655 (tp30) cc_final: 0.7368 (mm-30) REVERT: H 196 SER cc_start: 0.8345 (p) cc_final: 0.8002 (t) REVERT: H 217 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8233 (tppt) REVERT: N 16 SER cc_start: 0.7336 (p) cc_final: 0.6899 (p) REVERT: N 48 GLN cc_start: 0.5981 (tt0) cc_final: 0.4516 (tp40) REVERT: N 89 TYR cc_start: 0.6404 (m-80) cc_final: 0.5561 (m-80) REVERT: N 90 LEU cc_start: 0.6749 (tp) cc_final: 0.6326 (tp) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.2928 time to fit residues: 189.0321 Evaluate side-chains 256 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 69 ASN A 77 HIS A 135 HIS A 146 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS A 252 GLN B 222 ASN M 39 HIS M 64 HIS M 124 ASN M 218 ASN M 335 GLN L 91 GLN L 125 GLN ** H 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13781 Z= 0.262 Angle : 0.625 9.147 18716 Z= 0.314 Chirality : 0.044 0.166 2087 Planarity : 0.005 0.047 2363 Dihedral : 8.985 117.064 1952 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.94 % Allowed : 11.40 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.01 (0.19), residues: 1683 helix: -1.15 (0.23), residues: 427 sheet: -1.04 (0.27), residues: 349 loop : -1.51 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 119 HIS 0.008 0.001 HIS A 42 PHE 0.014 0.002 PHE A 279 TYR 0.030 0.002 TYR L 50 ARG 0.006 0.001 ARG G 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 286 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7930 (mtt) cc_final: 0.7170 (mtp) REVERT: A 99 SER cc_start: 0.8594 (m) cc_final: 0.8087 (t) REVERT: A 141 ASP cc_start: 0.7763 (t0) cc_final: 0.7511 (m-30) REVERT: A 220 HIS cc_start: 0.8132 (t70) cc_final: 0.7903 (t70) REVERT: A 226 LYS cc_start: 0.8223 (tttt) cc_final: 0.7934 (tptp) REVERT: A 268 GLU cc_start: 0.8711 (tp30) cc_final: 0.7827 (pm20) REVERT: A 417 ARG cc_start: 0.7420 (ttt90) cc_final: 0.7189 (ptm160) REVERT: A 536 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 249 SER cc_start: 0.7580 (t) cc_final: 0.7354 (p) REVERT: B 251 MET cc_start: 0.7473 (ttm) cc_final: 0.7221 (ttt) REVERT: B 261 LYS cc_start: 0.8712 (tptt) cc_final: 0.8506 (tppt) REVERT: G 87 THR cc_start: 0.9194 (p) cc_final: 0.8943 (p) REVERT: G 105 GLN cc_start: 0.7830 (mt0) cc_final: 0.7574 (tm-30) REVERT: G 106 ILE cc_start: 0.6571 (tt) cc_final: 0.6157 (tt) REVERT: G 119 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7698 (pt0) REVERT: G 147 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7015 (ptt90) REVERT: G 189 MET cc_start: 0.7671 (mmt) cc_final: 0.7121 (mmp) REVERT: G 198 ILE cc_start: 0.7963 (mt) cc_final: 0.7760 (mm) REVERT: G 201 TYR cc_start: 0.6977 (m-80) cc_final: 0.5900 (m-80) REVERT: G 206 MET cc_start: 0.7338 (mtm) cc_final: 0.6858 (ttm) REVERT: G 245 ASP cc_start: 0.8867 (m-30) cc_final: 0.8593 (m-30) REVERT: G 280 TYR cc_start: 0.6897 (m-80) cc_final: 0.6096 (m-80) REVERT: M 22 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6040 (tm-30) REVERT: M 42 LYS cc_start: 0.7391 (mmtm) cc_final: 0.6820 (mttp) REVERT: M 46 LYS cc_start: 0.7443 (mmtm) cc_final: 0.7158 (tppt) REVERT: M 55 ASP cc_start: 0.5687 (p0) cc_final: 0.5404 (t70) REVERT: M 171 TYR cc_start: 0.7601 (t80) cc_final: 0.7025 (t80) REVERT: M 195 LEU cc_start: 0.8029 (tp) cc_final: 0.7826 (tp) REVERT: M 355 GLN cc_start: 0.8648 (mt0) cc_final: 0.8127 (tt0) REVERT: M 356 THR cc_start: 0.8194 (p) cc_final: 0.7789 (t) REVERT: M 370 GLU cc_start: 0.8086 (tp30) cc_final: 0.7697 (tp30) REVERT: L 5 MET cc_start: 0.6026 (ptp) cc_final: 0.4442 (ppp) REVERT: L 25 ARG cc_start: 0.8416 (mtt-85) cc_final: 0.7617 (mmm160) REVERT: L 43 LYS cc_start: 0.8420 (tppt) cc_final: 0.7830 (mmmm) REVERT: L 71 ASP cc_start: 0.7711 (t70) cc_final: 0.7443 (t0) REVERT: L 101 GLN cc_start: 0.8597 (mm110) cc_final: 0.8202 (mm110) REVERT: L 117 PHE cc_start: 0.7575 (m-80) cc_final: 0.7359 (m-80) REVERT: L 123 ASP cc_start: 0.8216 (t0) cc_final: 0.7963 (p0) REVERT: L 143 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7369 (tpt90) REVERT: L 150 LYS cc_start: 0.8569 (mttt) cc_final: 0.8074 (mtmm) REVERT: L 196 GLU cc_start: 0.8186 (tt0) cc_final: 0.7229 (tp30) REVERT: H 210 TYR cc_start: 0.7849 (m-80) cc_final: 0.7473 (m-80) REVERT: N 48 GLN cc_start: 0.5975 (tt0) cc_final: 0.5088 (tp40) REVERT: N 92 MET cc_start: 0.7426 (mtm) cc_final: 0.7058 (mtm) outliers start: 43 outliers final: 27 residues processed: 316 average time/residue: 0.2457 time to fit residues: 112.0134 Evaluate side-chains 253 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 17 TYR Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.0170 chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 42 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 0.0020 chunk 52 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 overall best weight: 0.5228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 220 HIS B 222 ASN G 148 ASN G 222 GLN M 124 ASN ** M 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN ** H 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13781 Z= 0.154 Angle : 0.556 10.390 18716 Z= 0.270 Chirality : 0.042 0.147 2087 Planarity : 0.004 0.040 2363 Dihedral : 8.381 115.489 1952 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.94 % Allowed : 12.90 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.42 (0.20), residues: 1683 helix: -0.48 (0.25), residues: 417 sheet: -1.03 (0.27), residues: 366 loop : -1.06 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 10 HIS 0.005 0.001 HIS B 257 PHE 0.014 0.001 PHE M 250 TYR 0.018 0.001 TYR H 161 ARG 0.005 0.000 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 238 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7978 (mtt) cc_final: 0.7207 (mtp) REVERT: A 99 SER cc_start: 0.8585 (m) cc_final: 0.8101 (t) REVERT: A 226 LYS cc_start: 0.8259 (tttt) cc_final: 0.7978 (tptp) REVERT: A 268 GLU cc_start: 0.8680 (tp30) cc_final: 0.7832 (pm20) REVERT: A 417 ARG cc_start: 0.7412 (ttt90) cc_final: 0.7188 (ptm160) REVERT: A 432 TYR cc_start: 0.6640 (m-10) cc_final: 0.6393 (m-10) REVERT: A 536 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 249 SER cc_start: 0.7550 (t) cc_final: 0.7336 (p) REVERT: B 251 MET cc_start: 0.7578 (ttm) cc_final: 0.7306 (ttt) REVERT: G 39 TYR cc_start: 0.7220 (t80) cc_final: 0.7019 (t80) REVERT: G 87 THR cc_start: 0.9044 (p) cc_final: 0.8788 (p) REVERT: G 105 GLN cc_start: 0.7810 (mt0) cc_final: 0.7561 (tm-30) REVERT: G 119 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7612 (pt0) REVERT: G 189 MET cc_start: 0.7660 (mmt) cc_final: 0.6881 (mmm) REVERT: G 195 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7690 (tm-30) REVERT: G 206 MET cc_start: 0.7380 (mtm) cc_final: 0.6881 (ttm) REVERT: G 280 TYR cc_start: 0.6930 (m-80) cc_final: 0.6133 (m-80) REVERT: M 22 GLU cc_start: 0.6575 (mt-10) cc_final: 0.5857 (tm-30) REVERT: M 28 GLU cc_start: 0.8429 (tt0) cc_final: 0.7750 (pp20) REVERT: M 42 LYS cc_start: 0.7468 (mmtm) cc_final: 0.6874 (mttp) REVERT: M 46 LYS cc_start: 0.7374 (mmtm) cc_final: 0.7133 (tppt) REVERT: M 55 ASP cc_start: 0.5690 (p0) cc_final: 0.5304 (t70) REVERT: M 171 TYR cc_start: 0.7562 (t80) cc_final: 0.7002 (t80) REVERT: M 370 GLU cc_start: 0.7960 (tp30) cc_final: 0.7564 (tp30) REVERT: L 5 MET cc_start: 0.5978 (ptp) cc_final: 0.4508 (ppp) REVERT: L 25 ARG cc_start: 0.8416 (mtt-85) cc_final: 0.7629 (mmm160) REVERT: L 43 LYS cc_start: 0.8344 (tppt) cc_final: 0.7747 (mmmm) REVERT: L 71 ASP cc_start: 0.7649 (t70) cc_final: 0.7385 (t0) REVERT: L 101 GLN cc_start: 0.8585 (mm110) cc_final: 0.8130 (mm110) REVERT: L 143 ARG cc_start: 0.8093 (ttt-90) cc_final: 0.7375 (tpt90) REVERT: L 150 LYS cc_start: 0.8476 (mttt) cc_final: 0.8079 (mtmm) REVERT: H 16 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: H 164 GLU cc_start: 0.7845 (tp30) cc_final: 0.7374 (mm-30) REVERT: H 210 TYR cc_start: 0.7842 (m-80) cc_final: 0.7458 (m-80) REVERT: N 45 TRP cc_start: 0.7258 (m100) cc_final: 0.6918 (m-10) REVERT: N 48 GLN cc_start: 0.6041 (tt0) cc_final: 0.5154 (tp40) outliers start: 43 outliers final: 28 residues processed: 268 average time/residue: 0.2419 time to fit residues: 94.0688 Evaluate side-chains 236 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 124 ASN Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 0.0670 chunk 162 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN G 223 HIS M 39 HIS M 355 GLN ** M 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13781 Z= 0.263 Angle : 0.586 9.891 18716 Z= 0.288 Chirality : 0.043 0.177 2087 Planarity : 0.004 0.041 2363 Dihedral : 8.367 115.519 1952 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.16 % Allowed : 12.90 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.09 (0.20), residues: 1683 helix: -0.18 (0.26), residues: 411 sheet: -0.94 (0.26), residues: 394 loop : -0.79 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M 10 HIS 0.015 0.001 HIS A 37 PHE 0.015 0.002 PHE G 91 TYR 0.025 0.002 TYR L 50 ARG 0.007 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 221 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7881 (m-70) REVERT: A 95 MET cc_start: 0.7969 (mtt) cc_final: 0.7708 (mtm) REVERT: A 99 SER cc_start: 0.8765 (m) cc_final: 0.8317 (t) REVERT: A 226 LYS cc_start: 0.8352 (tttt) cc_final: 0.8059 (tptp) REVERT: A 268 GLU cc_start: 0.8786 (tp30) cc_final: 0.7874 (pm20) REVERT: A 417 ARG cc_start: 0.7338 (ttt90) cc_final: 0.7062 (ptm160) REVERT: A 536 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7792 (mt-10) REVERT: B 251 MET cc_start: 0.7746 (ttm) cc_final: 0.7427 (ttt) REVERT: G 83 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.8928 (m) REVERT: G 87 THR cc_start: 0.8965 (p) cc_final: 0.8681 (p) REVERT: G 105 GLN cc_start: 0.7950 (mt0) cc_final: 0.7662 (tm-30) REVERT: G 119 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8186 (mt-10) REVERT: G 206 MET cc_start: 0.7786 (mtm) cc_final: 0.7055 (mtm) REVERT: G 225 VAL cc_start: 0.9532 (m) cc_final: 0.9239 (p) REVERT: M 22 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6082 (tm-30) REVERT: M 28 GLU cc_start: 0.8456 (tt0) cc_final: 0.7803 (pp20) REVERT: M 46 LYS cc_start: 0.7390 (mmtm) cc_final: 0.7124 (tppt) REVERT: M 171 TYR cc_start: 0.7684 (t80) cc_final: 0.7154 (t80) REVERT: M 370 GLU cc_start: 0.7974 (tp30) cc_final: 0.7675 (tp30) REVERT: L 5 MET cc_start: 0.6231 (ptp) cc_final: 0.5807 (ptp) REVERT: L 25 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.7894 (ttm-80) REVERT: L 43 LYS cc_start: 0.8594 (tppt) cc_final: 0.8072 (mmmm) REVERT: L 71 ASP cc_start: 0.7679 (t70) cc_final: 0.7307 (t70) REVERT: L 101 GLN cc_start: 0.8584 (mm110) cc_final: 0.8133 (mm110) REVERT: L 117 PHE cc_start: 0.8152 (m-80) cc_final: 0.7608 (m-80) REVERT: L 143 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7389 (tpt90) REVERT: L 150 LYS cc_start: 0.8451 (mttt) cc_final: 0.8024 (mtmm) REVERT: H 16 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: H 210 TYR cc_start: 0.7892 (m-80) cc_final: 0.7567 (m-80) REVERT: N 91 GLN cc_start: 0.7531 (tp40) cc_final: 0.7249 (tp40) outliers start: 61 outliers final: 44 residues processed: 264 average time/residue: 0.2375 time to fit residues: 92.4549 Evaluate side-chains 234 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 187 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain M residue 341 TYR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS M 218 ASN ** M 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13781 Z= 0.187 Angle : 0.546 8.835 18716 Z= 0.268 Chirality : 0.042 0.225 2087 Planarity : 0.004 0.039 2363 Dihedral : 8.153 115.150 1952 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.34 % Allowed : 14.61 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.88 (0.21), residues: 1683 helix: -0.04 (0.26), residues: 414 sheet: -0.83 (0.26), residues: 391 loop : -0.62 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP M 10 HIS 0.020 0.001 HIS M 39 PHE 0.011 0.001 PHE M 250 TYR 0.017 0.001 TYR L 50 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 200 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8526 (mtp) cc_final: 0.8155 (mtp) REVERT: A 95 MET cc_start: 0.8011 (mtt) cc_final: 0.7719 (mtm) REVERT: A 99 SER cc_start: 0.8857 (m) cc_final: 0.8390 (t) REVERT: A 181 TYR cc_start: 0.7194 (m-80) cc_final: 0.6876 (m-80) REVERT: A 268 GLU cc_start: 0.8750 (tp30) cc_final: 0.7881 (pm20) REVERT: A 417 ARG cc_start: 0.7330 (ttt90) cc_final: 0.7059 (ptm160) REVERT: A 536 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 251 MET cc_start: 0.7733 (ttm) cc_final: 0.7395 (ttt) REVERT: G 83 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8924 (m) REVERT: G 87 THR cc_start: 0.8920 (p) cc_final: 0.8618 (p) REVERT: G 105 GLN cc_start: 0.7969 (mt0) cc_final: 0.7670 (tm-30) REVERT: G 119 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8175 (mt-10) REVERT: G 206 MET cc_start: 0.7794 (mtm) cc_final: 0.7057 (mtm) REVERT: G 225 VAL cc_start: 0.9504 (m) cc_final: 0.9167 (p) REVERT: M 22 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6086 (tm-30) REVERT: M 28 GLU cc_start: 0.8402 (tt0) cc_final: 0.7758 (pp20) REVERT: M 171 TYR cc_start: 0.7583 (t80) cc_final: 0.7038 (t80) REVERT: M 370 GLU cc_start: 0.7800 (tp30) cc_final: 0.7488 (tp30) REVERT: L 5 MET cc_start: 0.6195 (ptp) cc_final: 0.5806 (ptp) REVERT: L 25 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.7879 (ttm-80) REVERT: L 43 LYS cc_start: 0.8516 (tppt) cc_final: 0.7961 (mmmm) REVERT: L 71 ASP cc_start: 0.7739 (t70) cc_final: 0.7356 (t70) REVERT: L 101 GLN cc_start: 0.8582 (mm110) cc_final: 0.8123 (mm110) REVERT: L 117 PHE cc_start: 0.8042 (m-80) cc_final: 0.7803 (m-80) REVERT: L 143 ARG cc_start: 0.8144 (ttt-90) cc_final: 0.7296 (tpt90) REVERT: L 150 LYS cc_start: 0.8402 (mttt) cc_final: 0.8024 (mtmm) REVERT: L 196 GLU cc_start: 0.8306 (tt0) cc_final: 0.7506 (tp30) REVERT: N 43 MET cc_start: 0.6754 (mtt) cc_final: 0.6498 (mmp) REVERT: N 45 TRP cc_start: 0.7351 (m100) cc_final: 0.7023 (m-10) outliers start: 49 outliers final: 32 residues processed: 236 average time/residue: 0.2334 time to fit residues: 81.5747 Evaluate side-chains 220 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 341 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN M 203 HIS M 218 ASN ** M 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13781 Z= 0.331 Angle : 0.633 9.959 18716 Z= 0.317 Chirality : 0.044 0.167 2087 Planarity : 0.004 0.039 2363 Dihedral : 8.418 115.089 1952 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.10 % Allowed : 14.33 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.92 (0.21), residues: 1683 helix: -0.09 (0.26), residues: 413 sheet: -0.86 (0.26), residues: 396 loop : -0.63 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 45 HIS 0.023 0.002 HIS B 257 PHE 0.021 0.002 PHE G 91 TYR 0.031 0.002 TYR H 97 ARG 0.014 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 202 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8497 (mtp) cc_final: 0.8165 (mtp) REVERT: A 237 GLN cc_start: 0.9235 (mp10) cc_final: 0.7927 (pp30) REVERT: A 268 GLU cc_start: 0.8865 (tp30) cc_final: 0.7868 (pm20) REVERT: A 417 ARG cc_start: 0.7349 (ttt90) cc_final: 0.7102 (ptm160) REVERT: B 251 MET cc_start: 0.7782 (ttm) cc_final: 0.7432 (ttt) REVERT: G 83 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9013 (m) REVERT: G 87 THR cc_start: 0.8889 (p) cc_final: 0.8537 (p) REVERT: G 105 GLN cc_start: 0.8172 (mt0) cc_final: 0.7937 (tm-30) REVERT: G 206 MET cc_start: 0.7966 (mtm) cc_final: 0.7152 (mtm) REVERT: G 225 VAL cc_start: 0.9475 (m) cc_final: 0.9122 (p) REVERT: M 22 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6027 (tm-30) REVERT: M 171 TYR cc_start: 0.7563 (t80) cc_final: 0.7035 (t80) REVERT: M 370 GLU cc_start: 0.7822 (tp30) cc_final: 0.7395 (tp30) REVERT: L 25 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.7844 (ttm-80) REVERT: L 43 LYS cc_start: 0.8660 (tppt) cc_final: 0.8066 (mmmm) REVERT: L 71 ASP cc_start: 0.7770 (t70) cc_final: 0.7450 (t0) REVERT: L 91 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: L 101 GLN cc_start: 0.8598 (mm110) cc_final: 0.8181 (mm110) REVERT: L 117 PHE cc_start: 0.8218 (m-80) cc_final: 0.7878 (m-80) REVERT: L 143 ARG cc_start: 0.8212 (ttt-90) cc_final: 0.7377 (tpt90) REVERT: L 150 LYS cc_start: 0.8335 (mttt) cc_final: 0.7931 (mtmm) REVERT: L 196 GLU cc_start: 0.8302 (tt0) cc_final: 0.7440 (tp30) REVERT: H 210 TYR cc_start: 0.7794 (m-80) cc_final: 0.7556 (m-80) REVERT: H 211 ILE cc_start: 0.8848 (mm) cc_final: 0.8539 (mm) outliers start: 60 outliers final: 43 residues processed: 245 average time/residue: 0.2297 time to fit residues: 84.9777 Evaluate side-chains 226 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 258 PHE Chi-restraints excluded: chain M residue 341 TYR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 220 ASN Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 91 optimal weight: 0.0870 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS B 257 HIS G 36 HIS M 218 ASN M 367 ASN H 87 ASN N 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13781 Z= 0.159 Angle : 0.545 7.593 18716 Z= 0.267 Chirality : 0.042 0.156 2087 Planarity : 0.004 0.052 2363 Dihedral : 8.070 114.148 1952 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.66 % Allowed : 17.06 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.76 (0.21), residues: 1683 helix: 0.08 (0.26), residues: 413 sheet: -0.77 (0.26), residues: 381 loop : -0.56 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M 10 HIS 0.008 0.001 HIS G 268 PHE 0.012 0.001 PHE M 250 TYR 0.015 0.001 TYR H 118 ARG 0.006 0.000 ARG N 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8296 (tpp-160) cc_final: 0.7647 (mtm180) REVERT: A 93 MET cc_start: 0.8504 (mtp) cc_final: 0.8139 (mtp) REVERT: A 181 TYR cc_start: 0.7424 (m-80) cc_final: 0.7117 (m-80) REVERT: A 268 GLU cc_start: 0.8758 (tp30) cc_final: 0.7992 (pm20) REVERT: A 417 ARG cc_start: 0.7399 (ttt90) cc_final: 0.7144 (ptm160) REVERT: A 433 TYR cc_start: 0.7926 (t80) cc_final: 0.7624 (t80) REVERT: A 453 LEU cc_start: 0.7835 (mp) cc_final: 0.7144 (tp) REVERT: B 251 MET cc_start: 0.7789 (ttm) cc_final: 0.7421 (ttt) REVERT: G 83 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8910 (m) REVERT: G 85 MET cc_start: 0.8582 (tpp) cc_final: 0.8349 (tpp) REVERT: G 87 THR cc_start: 0.8887 (p) cc_final: 0.8556 (p) REVERT: G 105 GLN cc_start: 0.8105 (mt0) cc_final: 0.7894 (tm-30) REVERT: G 206 MET cc_start: 0.7987 (mtm) cc_final: 0.7171 (mtm) REVERT: G 225 VAL cc_start: 0.9462 (m) cc_final: 0.9090 (p) REVERT: M 22 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6064 (tm-30) REVERT: M 62 TRP cc_start: 0.7589 (t-100) cc_final: 0.6288 (t-100) REVERT: M 171 TYR cc_start: 0.7543 (t80) cc_final: 0.7044 (t80) REVERT: M 365 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7895 (tm-30) REVERT: M 370 GLU cc_start: 0.7718 (tp30) cc_final: 0.7365 (tp30) REVERT: L 25 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.7849 (ttm-80) REVERT: L 43 LYS cc_start: 0.8522 (tppt) cc_final: 0.7945 (mmmm) REVERT: L 71 ASP cc_start: 0.7747 (t70) cc_final: 0.7323 (t70) REVERT: L 98 THR cc_start: 0.8611 (p) cc_final: 0.8135 (p) REVERT: L 101 GLN cc_start: 0.8566 (mm110) cc_final: 0.8088 (mm110) REVERT: L 143 ARG cc_start: 0.8154 (ttt-90) cc_final: 0.7333 (tpt90) REVERT: L 150 LYS cc_start: 0.8268 (mttt) cc_final: 0.7939 (mtmm) REVERT: L 196 GLU cc_start: 0.8306 (tt0) cc_final: 0.7503 (tp30) REVERT: H 22 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.6925 (ttt-90) REVERT: H 164 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7839 (mm-30) REVERT: H 210 TYR cc_start: 0.7813 (m-80) cc_final: 0.7501 (m-80) REVERT: H 224 ASP cc_start: 0.8211 (m-30) cc_final: 0.6666 (p0) outliers start: 39 outliers final: 29 residues processed: 230 average time/residue: 0.2271 time to fit residues: 78.6412 Evaluate side-chains 213 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 341 TYR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 0.0470 chunk 96 optimal weight: 0.0060 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 257 HIS M 39 HIS M 218 ASN H 87 ASN N 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13781 Z= 0.295 Angle : 0.598 7.416 18716 Z= 0.297 Chirality : 0.043 0.178 2087 Planarity : 0.004 0.040 2363 Dihedral : 8.279 114.447 1952 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.21 % Allowed : 17.06 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.74 (0.21), residues: 1683 helix: 0.07 (0.26), residues: 412 sheet: -0.78 (0.26), residues: 392 loop : -0.51 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP M 10 HIS 0.023 0.001 HIS B 257 PHE 0.023 0.002 PHE L 210 TYR 0.023 0.002 TYR H 97 ARG 0.005 0.001 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 183 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.7635 (mtm180) REVERT: A 93 MET cc_start: 0.8504 (mtp) cc_final: 0.8184 (mtp) REVERT: A 268 GLU cc_start: 0.8811 (tp30) cc_final: 0.7861 (pm20) REVERT: A 417 ARG cc_start: 0.7450 (ttt90) cc_final: 0.7199 (ptm160) REVERT: A 425 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7162 (mp0) REVERT: B 235 HIS cc_start: 0.7203 (m-70) cc_final: 0.6435 (t70) REVERT: B 251 MET cc_start: 0.7753 (ttm) cc_final: 0.7386 (ttt) REVERT: G 83 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8947 (m) REVERT: G 85 MET cc_start: 0.8600 (tpp) cc_final: 0.8294 (tpp) REVERT: G 105 GLN cc_start: 0.8151 (mt0) cc_final: 0.7926 (tm-30) REVERT: G 206 MET cc_start: 0.7990 (mtm) cc_final: 0.7174 (mtm) REVERT: G 225 VAL cc_start: 0.9486 (m) cc_final: 0.9141 (p) REVERT: M 22 GLU cc_start: 0.6544 (mt-10) cc_final: 0.5898 (tm-30) REVERT: M 62 TRP cc_start: 0.7682 (t-100) cc_final: 0.6483 (t-100) REVERT: M 171 TYR cc_start: 0.7729 (t80) cc_final: 0.7257 (t80) REVERT: M 370 GLU cc_start: 0.7646 (tp30) cc_final: 0.7330 (tp30) REVERT: L 25 ARG cc_start: 0.8367 (mtt-85) cc_final: 0.7910 (mtp85) REVERT: L 43 LYS cc_start: 0.8567 (tppt) cc_final: 0.8001 (mmmm) REVERT: L 71 ASP cc_start: 0.7789 (t70) cc_final: 0.7518 (t70) REVERT: L 91 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: L 98 THR cc_start: 0.8664 (p) cc_final: 0.8002 (p) REVERT: L 101 GLN cc_start: 0.8595 (mm110) cc_final: 0.8142 (mm110) REVERT: L 143 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7372 (tpt90) REVERT: L 150 LYS cc_start: 0.8256 (mttt) cc_final: 0.7912 (mtmm) REVERT: L 196 GLU cc_start: 0.8322 (tt0) cc_final: 0.7478 (tp30) REVERT: N 45 TRP cc_start: 0.7177 (m100) cc_final: 0.6969 (m-10) outliers start: 47 outliers final: 38 residues processed: 218 average time/residue: 0.2394 time to fit residues: 78.3498 Evaluate side-chains 213 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 258 PHE Chi-restraints excluded: chain M residue 341 TYR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 0.0370 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 0.0870 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS M 218 ASN H 180 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13781 Z= 0.158 Angle : 0.553 7.070 18716 Z= 0.272 Chirality : 0.042 0.175 2087 Planarity : 0.004 0.077 2363 Dihedral : 8.074 114.246 1952 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.66 % Allowed : 17.61 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.67 (0.21), residues: 1683 helix: 0.15 (0.26), residues: 412 sheet: -0.77 (0.27), residues: 383 loop : -0.46 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 10 HIS 0.007 0.001 HIS G 268 PHE 0.021 0.001 PHE L 117 TYR 0.017 0.001 TYR G 272 ARG 0.004 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8298 (tpp-160) cc_final: 0.7643 (mtm180) REVERT: A 181 TYR cc_start: 0.7426 (m-80) cc_final: 0.7156 (m-80) REVERT: A 268 GLU cc_start: 0.8774 (tp30) cc_final: 0.8008 (pm20) REVERT: A 417 ARG cc_start: 0.7447 (ttt90) cc_final: 0.7196 (ptm160) REVERT: A 453 LEU cc_start: 0.8076 (mp) cc_final: 0.7308 (tp) REVERT: B 235 HIS cc_start: 0.7068 (m-70) cc_final: 0.6395 (t70) REVERT: B 251 MET cc_start: 0.7735 (ttm) cc_final: 0.7369 (ttt) REVERT: G 83 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8929 (m) REVERT: G 85 MET cc_start: 0.8570 (tpp) cc_final: 0.8337 (tpp) REVERT: G 87 THR cc_start: 0.8894 (p) cc_final: 0.8557 (p) REVERT: G 105 GLN cc_start: 0.8104 (mt0) cc_final: 0.7875 (tm-30) REVERT: G 206 MET cc_start: 0.7960 (mtm) cc_final: 0.7152 (mtm) REVERT: G 225 VAL cc_start: 0.9484 (m) cc_final: 0.9134 (p) REVERT: G 239 ASP cc_start: 0.7347 (t0) cc_final: 0.6987 (t0) REVERT: M 22 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6019 (tm-30) REVERT: M 62 TRP cc_start: 0.7610 (t-100) cc_final: 0.6398 (t-100) REVERT: M 171 TYR cc_start: 0.7563 (t80) cc_final: 0.7133 (t80) REVERT: M 370 GLU cc_start: 0.7440 (tp30) cc_final: 0.7114 (tp30) REVERT: L 25 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.7781 (ttm-80) REVERT: L 43 LYS cc_start: 0.8475 (tppt) cc_final: 0.7911 (mmmm) REVERT: L 71 ASP cc_start: 0.7789 (t70) cc_final: 0.7510 (t70) REVERT: L 101 GLN cc_start: 0.8562 (mm110) cc_final: 0.8103 (mm110) REVERT: L 143 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7275 (tpt90) REVERT: L 150 LYS cc_start: 0.8233 (mttt) cc_final: 0.7916 (mtmm) REVERT: L 196 GLU cc_start: 0.8302 (tt0) cc_final: 0.7476 (tp30) outliers start: 39 outliers final: 33 residues processed: 219 average time/residue: 0.2317 time to fit residues: 76.2922 Evaluate side-chains 220 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 341 TYR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 218 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13781 Z= 0.219 Angle : 0.577 7.464 18716 Z= 0.286 Chirality : 0.042 0.191 2087 Planarity : 0.004 0.078 2363 Dihedral : 8.148 114.219 1952 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.59 % Allowed : 17.88 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.61 (0.21), residues: 1683 helix: 0.20 (0.26), residues: 412 sheet: -0.71 (0.27), residues: 379 loop : -0.45 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 170 HIS 0.010 0.001 HIS A 220 PHE 0.026 0.002 PHE M 258 TYR 0.018 0.001 TYR L 50 ARG 0.011 0.000 ARG B 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8280 (tpp-160) cc_final: 0.7636 (mtm180) REVERT: A 93 MET cc_start: 0.8515 (mtm) cc_final: 0.8224 (mtm) REVERT: A 256 MET cc_start: 0.8011 (ttp) cc_final: 0.7684 (ttm) REVERT: A 268 GLU cc_start: 0.8820 (tp30) cc_final: 0.7909 (pm20) REVERT: A 417 ARG cc_start: 0.7480 (ttt90) cc_final: 0.7228 (ptm160) REVERT: A 425 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7168 (mp0) REVERT: A 432 TYR cc_start: 0.6683 (m-10) cc_final: 0.6378 (m-10) REVERT: A 453 LEU cc_start: 0.8219 (mp) cc_final: 0.7235 (tp) REVERT: B 251 MET cc_start: 0.7736 (ttm) cc_final: 0.7364 (ttt) REVERT: G 83 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8926 (m) REVERT: G 85 MET cc_start: 0.8633 (tpp) cc_final: 0.8366 (tpp) REVERT: G 87 THR cc_start: 0.8876 (p) cc_final: 0.8538 (p) REVERT: G 105 GLN cc_start: 0.8106 (mt0) cc_final: 0.7886 (tm-30) REVERT: G 206 MET cc_start: 0.7968 (mtm) cc_final: 0.7154 (mtm) REVERT: G 225 VAL cc_start: 0.9513 (m) cc_final: 0.9176 (p) REVERT: G 239 ASP cc_start: 0.7346 (t0) cc_final: 0.6986 (t0) REVERT: M 22 GLU cc_start: 0.6613 (mt-10) cc_final: 0.5983 (tm-30) REVERT: M 62 TRP cc_start: 0.7617 (t-100) cc_final: 0.6324 (t-100) REVERT: M 171 TYR cc_start: 0.7566 (t80) cc_final: 0.7181 (t80) REVERT: M 370 GLU cc_start: 0.7465 (tp30) cc_final: 0.7129 (tp30) REVERT: L 25 ARG cc_start: 0.8469 (mtt-85) cc_final: 0.7774 (ttm-80) REVERT: L 43 LYS cc_start: 0.8495 (tppt) cc_final: 0.7930 (mmmm) REVERT: L 71 ASP cc_start: 0.7849 (t70) cc_final: 0.7552 (t70) REVERT: L 101 GLN cc_start: 0.8582 (mm110) cc_final: 0.8131 (mm110) REVERT: L 134 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8546 (p) REVERT: L 143 ARG cc_start: 0.8180 (ttt-90) cc_final: 0.7285 (tpt90) REVERT: L 150 LYS cc_start: 0.8213 (mttt) cc_final: 0.7890 (mtmm) REVERT: L 196 GLU cc_start: 0.8314 (tt0) cc_final: 0.7476 (tp30) REVERT: H 110 TYR cc_start: 0.8184 (p90) cc_final: 0.7979 (p90) REVERT: H 164 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7819 (mm-30) REVERT: N 45 TRP cc_start: 0.6077 (m-10) cc_final: 0.5678 (m-10) outliers start: 38 outliers final: 35 residues processed: 210 average time/residue: 0.2286 time to fit residues: 71.3983 Evaluate side-chains 219 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 341 TYR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.2980 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 133 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS M 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.144561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.111532 restraints weight = 25911.700| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.93 r_work: 0.3420 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13781 Z= 0.170 Angle : 0.575 15.784 18716 Z= 0.282 Chirality : 0.042 0.218 2087 Planarity : 0.004 0.074 2363 Dihedral : 8.072 114.180 1952 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.59 % Allowed : 17.82 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.56 (0.21), residues: 1683 helix: 0.28 (0.26), residues: 413 sheet: -0.69 (0.27), residues: 377 loop : -0.43 (0.22), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP H 170 HIS 0.009 0.001 HIS A 152 PHE 0.021 0.001 PHE M 258 TYR 0.016 0.001 TYR G 272 ARG 0.004 0.000 ARG N 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.30 seconds wall clock time: 57 minutes 40.13 seconds (3460.13 seconds total)