Starting phenix.real_space_refine on Fri Mar 22 13:13:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcu_28993/03_2024/8fcu_28993_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcu_28993/03_2024/8fcu_28993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcu_28993/03_2024/8fcu_28993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcu_28993/03_2024/8fcu_28993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcu_28993/03_2024/8fcu_28993_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcu_28993/03_2024/8fcu_28993_updated.pdb" } resolution = 3.19 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= 0.069 sd= 0.876 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 859 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 159 5.49 5 Mg 1 5.21 5 S 121 5.16 5 C 20442 2.51 5 N 5567 2.21 5 O 6402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "H TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 251": "OE1" <-> "OE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 194": "OE1" <-> "OE2" Residue "I GLU 235": "OE1" <-> "OE2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "I GLU 446": "OE1" <-> "OE2" Residue "I GLU 468": "OE1" <-> "OE2" Residue "I GLU 471": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L GLU 35": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "P GLU 25": "OE1" <-> "OE2" Residue "P GLU 72": "OE1" <-> "OE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 326": "OE1" <-> "OE2" Residue "Q GLU 10": "OE1" <-> "OE2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q GLU 210": "OE1" <-> "OE2" Residue "Q PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32692 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1702 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2330 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "H" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 26, 'rna3p': 36} Chain: "N" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1282 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "O" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 620 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "P" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2618 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain: "Q" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2508 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.42, per 1000 atoms: 0.56 Number of scatterers: 32692 At special positions: 0 Unit cell: (105.4, 168.64, 254.014, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 121 16.00 P 159 15.00 Mg 1 11.99 O 6402 8.00 N 5567 7.00 C 20442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.61 Conformation dependent library (CDL) restraints added in 4.7 seconds 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 42 sheets defined 37.1% alpha, 12.8% beta 56 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 13.48 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 84 through 87 No H-bonds generated for 'chain 'B' and resid 84 through 87' Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 186 through 195 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 57 through 70 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 194 through 205 removed outlier: 3.623A pdb=" N ILE C 197 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Proline residue: C 199 - end of helix Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.610A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 57 through 70 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 194 through 205 removed outlier: 3.517A pdb=" N ILE D 197 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 198 " --> pdb=" O SER D 195 " (cutoff:3.500A) Proline residue: D 199 - end of helix Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 292 through 295 Processing helix chain 'D' and resid 302 through 317 Processing helix chain 'E' and resid 57 through 70 Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 194 through 205 Proline residue: E 199 - end of helix Processing helix chain 'E' and resid 256 through 263 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 277 through 284 Processing helix chain 'E' and resid 292 through 295 Processing helix chain 'E' and resid 302 through 317 Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 57 through 70 Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 194 through 205 removed outlier: 3.519A pdb=" N ILE F 197 " --> pdb=" O PHE F 194 " (cutoff:3.500A) Proline residue: F 199 - end of helix Processing helix chain 'F' and resid 257 through 264 Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.642A pdb=" N GLN F 283 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 295 Processing helix chain 'F' and resid 302 through 317 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 57 through 71 Processing helix chain 'G' and resid 99 through 103 Processing helix chain 'G' and resid 194 through 205 Proline residue: G 199 - end of helix Processing helix chain 'G' and resid 256 through 264 Processing helix chain 'G' and resid 269 through 271 No H-bonds generated for 'chain 'G' and resid 269 through 271' Processing helix chain 'G' and resid 277 through 283 Processing helix chain 'G' and resid 292 through 295 Processing helix chain 'G' and resid 302 through 316 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 57 through 70 Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 194 through 205 removed outlier: 3.777A pdb=" N ILE H 197 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) Proline residue: H 199 - end of helix Processing helix chain 'H' and resid 256 through 264 Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'H' and resid 277 through 283 Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 302 through 317 Processing helix chain 'I' and resid 20 through 39 Processing helix chain 'I' and resid 67 through 78 Processing helix chain 'I' and resid 99 through 112 Processing helix chain 'I' and resid 148 through 156 removed outlier: 3.668A pdb=" N PHE I 152 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA I 153 " --> pdb=" O GLN I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 186 No H-bonds generated for 'chain 'I' and resid 184 through 186' Processing helix chain 'I' and resid 196 through 208 Proline residue: I 206 - end of helix Processing helix chain 'I' and resid 239 through 251 removed outlier: 4.042A pdb=" N GLN I 251 " --> pdb=" O TRP I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 257 No H-bonds generated for 'chain 'I' and resid 254 through 257' Processing helix chain 'I' and resid 262 through 269 Processing helix chain 'I' and resid 312 through 324 Processing helix chain 'I' and resid 343 through 354 Processing helix chain 'I' and resid 358 through 360 No H-bonds generated for 'chain 'I' and resid 358 through 360' Processing helix chain 'I' and resid 362 through 366 Processing helix chain 'I' and resid 374 through 392 removed outlier: 3.957A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY I 385 " --> pdb=" O SER I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 420 removed outlier: 3.641A pdb=" N GLN I 398 " --> pdb=" O GLU I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 442 Processing helix chain 'I' and resid 446 through 460 Processing helix chain 'I' and resid 464 through 468 Processing helix chain 'I' and resid 470 through 479 Processing helix chain 'I' and resid 482 through 494 Processing helix chain 'J' and resid 6 through 32 Processing helix chain 'J' and resid 42 through 53 Processing helix chain 'J' and resid 59 through 72 removed outlier: 6.086A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 Processing helix chain 'J' and resid 82 through 90 Processing helix chain 'J' and resid 94 through 107 Processing helix chain 'J' and resid 109 through 111 No H-bonds generated for 'chain 'J' and resid 109 through 111' Processing helix chain 'K' and resid 6 through 32 Processing helix chain 'K' and resid 42 through 53 Processing helix chain 'K' and resid 59 through 72 removed outlier: 6.029A pdb=" N TYR K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 Processing helix chain 'K' and resid 83 through 90 Processing helix chain 'K' and resid 94 through 108 Processing helix chain 'L' and resid 6 through 32 Processing helix chain 'L' and resid 42 through 54 Processing helix chain 'L' and resid 58 through 72 Processing helix chain 'L' and resid 76 through 80 Processing helix chain 'L' and resid 83 through 91 Processing helix chain 'L' and resid 94 through 106 Processing helix chain 'P' and resid 37 through 47 Processing helix chain 'P' and resid 52 through 64 removed outlier: 4.670A pdb=" N ALA P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Proline residue: P 62 - end of helix Processing helix chain 'P' and resid 70 through 75 removed outlier: 4.048A pdb=" N SER P 75 " --> pdb=" O SER P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 82 removed outlier: 3.713A pdb=" N LEU P 82 " --> pdb=" O SER P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 92 Processing helix chain 'P' and resid 96 through 108 Processing helix chain 'P' and resid 114 through 117 Processing helix chain 'P' and resid 120 through 122 No H-bonds generated for 'chain 'P' and resid 120 through 122' Processing helix chain 'P' and resid 140 through 148 Processing helix chain 'P' and resid 157 through 160 Processing helix chain 'P' and resid 215 through 234 removed outlier: 4.557A pdb=" N VAL P 219 " --> pdb=" O GLU P 215 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN P 220 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR P 231 " --> pdb=" O LEU P 227 " (cutoff:3.500A) Proline residue: P 232 - end of helix Processing helix chain 'P' and resid 240 through 260 Processing helix chain 'P' and resid 263 through 280 removed outlier: 4.385A pdb=" N GLY P 269 " --> pdb=" O GLY P 266 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY P 270 " --> pdb=" O ASP P 267 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 271 " --> pdb=" O LEU P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 289 through 299 removed outlier: 4.825A pdb=" N ILE P 294 " --> pdb=" O VAL P 290 " (cutoff:3.500A) Proline residue: P 295 - end of helix Processing helix chain 'P' and resid 304 through 309 Processing helix chain 'P' and resid 312 through 322 Processing helix chain 'Q' and resid 9 through 12 removed outlier: 3.716A pdb=" N LEU Q 12 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 9 through 12' Processing helix chain 'Q' and resid 16 through 25 Processing helix chain 'Q' and resid 31 through 45 Processing helix chain 'Q' and resid 63 through 82 Proline residue: Q 80 - end of helix Processing helix chain 'Q' and resid 106 through 116 Processing helix chain 'Q' and resid 150 through 163 Processing helix chain 'Q' and resid 173 through 177 Processing helix chain 'Q' and resid 182 through 199 removed outlier: 4.237A pdb=" N GLN Q 186 " --> pdb=" O GLY Q 182 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU Q 189 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET Q 198 " --> pdb=" O SER Q 194 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR Q 199 " --> pdb=" O LEU Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 213 No H-bonds generated for 'chain 'Q' and resid 211 through 213' Processing helix chain 'Q' and resid 218 through 223 Processing helix chain 'Q' and resid 238 through 253 Processing helix chain 'Q' and resid 265 through 272 removed outlier: 4.661A pdb=" N GLU Q 268 " --> pdb=" O ASP Q 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 278 through 294 Processing helix chain 'Q' and resid 302 through 307 Processing helix chain 'Q' and resid 312 through 330 Processing sheet with id= A, first strand: chain 'A' and resid 147 through 150 Processing sheet with id= B, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.984A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.600A pdb=" N ARG A 160 " --> pdb=" O MET A 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 171 through 176 removed outlier: 6.915A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 105 through 108 removed outlier: 4.490A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 18 through 20 Processing sheet with id= G, first strand: chain 'B' and resid 208 through 210 Processing sheet with id= H, first strand: chain 'B' and resid 160 through 165 Processing sheet with id= I, first strand: chain 'C' and resid 297 through 299 removed outlier: 3.665A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= K, first strand: chain 'C' and resid 43 through 45 Processing sheet with id= L, first strand: chain 'C' and resid 77 through 79 Processing sheet with id= M, first strand: chain 'C' and resid 155 through 162 Processing sheet with id= N, first strand: chain 'D' and resid 297 through 299 removed outlier: 3.610A pdb=" N GLY D 276 " --> pdb=" O TYR D 299 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 225 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 25 through 27 Processing sheet with id= P, first strand: chain 'D' and resid 43 through 45 Processing sheet with id= Q, first strand: chain 'D' and resid 77 through 79 Processing sheet with id= R, first strand: chain 'E' and resid 297 through 299 removed outlier: 3.546A pdb=" N GLY E 276 " --> pdb=" O TYR E 299 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER E 225 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 25 through 27 Processing sheet with id= T, first strand: chain 'E' and resid 77 through 79 Processing sheet with id= U, first strand: chain 'E' and resid 155 through 159 Processing sheet with id= V, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.565A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 140 through 142 removed outlier: 3.604A pdb=" N TYR F 182 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 225 " --> pdb=" O LEU F 21 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS F 297 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLY F 276 " --> pdb=" O HIS F 297 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR F 299 " --> pdb=" O GLY F 276 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 43 through 45 Processing sheet with id= Y, first strand: chain 'F' and resid 77 through 79 Processing sheet with id= Z, first strand: chain 'F' and resid 155 through 158 Processing sheet with id= AA, first strand: chain 'G' and resid 145 through 147 removed outlier: 4.656A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 225 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS G 297 " --> pdb=" O ILE G 274 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLY G 276 " --> pdb=" O HIS G 297 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR G 299 " --> pdb=" O GLY G 276 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.782A pdb=" N GLY G 25 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 43 through 45 Processing sheet with id= AD, first strand: chain 'G' and resid 77 through 80 Processing sheet with id= AE, first strand: chain 'G' and resid 155 through 159 Processing sheet with id= AF, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.309A pdb=" N HIS H 297 " --> pdb=" O ILE H 274 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY H 276 " --> pdb=" O HIS H 297 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR H 299 " --> pdb=" O GLY H 276 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 24 through 27 Processing sheet with id= AH, first strand: chain 'H' and resid 43 through 45 Processing sheet with id= AI, first strand: chain 'H' and resid 77 through 80 Processing sheet with id= AJ, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.081A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 61 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 11 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= AL, first strand: chain 'I' and resid 125 through 132 Processing sheet with id= AM, first strand: chain 'I' and resid 210 through 214 removed outlier: 4.485A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 120 through 122 Processing sheet with id= AO, first strand: chain 'Q' and resid 55 through 57 removed outlier: 7.220A pdb=" N ILE Q 228 " --> pdb=" O TYR Q 56 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'Q' and resid 91 through 95 removed outlier: 6.175A pdb=" N VAL Q 167 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE Q 94 " --> pdb=" O VAL Q 167 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE Q 169 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU Q 202 " --> pdb=" O PHE Q 168 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL Q 170 " --> pdb=" O LEU Q 202 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N CYS Q 204 " --> pdb=" O VAL Q 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP 1073 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 11.31 Time building geometry restraints manager: 15.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9809 1.34 - 1.46: 9111 1.46 - 1.59: 14378 1.59 - 1.71: 309 1.71 - 1.84: 187 Bond restraints: 33794 Sorted by residual: bond pdb=" C SER A 199 " pdb=" N PRO A 200 " ideal model delta sigma weight residual 1.329 1.355 -0.026 1.18e-02 7.18e+03 4.91e+00 bond pdb=" O3' DC N 50 " pdb=" P DT N 51 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.44e+00 bond pdb=" CA ASP D 246 " pdb=" C ASP D 246 " ideal model delta sigma weight residual 1.524 1.508 0.016 8.10e-03 1.52e+04 3.68e+00 bond pdb=" O5' U M 20 " pdb=" C5' U M 20 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.74e+00 bond pdb=" C LEU I 379 " pdb=" O LEU I 379 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.15e-02 7.56e+03 2.58e+00 ... (remaining 33789 not shown) Histogram of bond angle deviations from ideal: 94.92 - 103.90: 791 103.90 - 112.89: 18237 112.89 - 121.88: 20246 121.88 - 130.87: 6873 130.87 - 139.86: 204 Bond angle restraints: 46351 Sorted by residual: angle pdb=" C4' G M 3 " pdb=" C3' G M 3 " pdb=" O3' G M 3 " ideal model delta sigma weight residual 109.40 117.22 -7.82 1.50e+00 4.44e-01 2.72e+01 angle pdb=" O3' DA N 23 " pdb=" C3' DA N 23 " pdb=" C2' DA N 23 " ideal model delta sigma weight residual 111.50 104.03 7.47 1.50e+00 4.44e-01 2.48e+01 angle pdb=" N LEU J 103 " pdb=" CA LEU J 103 " pdb=" C LEU J 103 " ideal model delta sigma weight residual 110.97 105.85 5.12 1.09e+00 8.42e-01 2.20e+01 angle pdb=" N TYR K 108 " pdb=" CA TYR K 108 " pdb=" C TYR K 108 " ideal model delta sigma weight residual 112.90 107.11 5.79 1.31e+00 5.83e-01 1.96e+01 angle pdb=" C THR B 157 " pdb=" N PRO B 158 " pdb=" CA PRO B 158 " ideal model delta sigma weight residual 119.76 115.32 4.44 1.03e+00 9.43e-01 1.86e+01 ... (remaining 46346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 18971 35.81 - 71.62: 1017 71.62 - 107.43: 61 107.43 - 143.24: 4 143.24 - 179.05: 5 Dihedral angle restraints: 20058 sinusoidal: 9538 harmonic: 10520 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 20.95 179.05 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 58.37 141.63 1 1.50e+01 4.44e-03 7.61e+01 dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual 232.00 66.54 165.46 1 1.70e+01 3.46e-03 6.54e+01 ... (remaining 20055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4011 0.045 - 0.091: 765 0.091 - 0.136: 209 0.136 - 0.182: 20 0.182 - 0.227: 6 Chirality restraints: 5011 Sorted by residual: chirality pdb=" C3' A M 38 " pdb=" C4' A M 38 " pdb=" O3' A M 38 " pdb=" C2' A M 38 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE J 13 " pdb=" CA ILE J 13 " pdb=" CG1 ILE J 13 " pdb=" CG2 ILE J 13 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE H 267 " pdb=" CA ILE H 267 " pdb=" CG1 ILE H 267 " pdb=" CG2 ILE H 267 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 5008 not shown) Planarity restraints: 5356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO F 247 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C PHE J 61 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 61 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C PHE K 61 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE K 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS K 62 " -0.018 2.00e-02 2.50e+03 ... (remaining 5353 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 416 2.58 - 3.16: 28142 3.16 - 3.74: 55287 3.74 - 4.32: 76700 4.32 - 4.90: 121525 Nonbonded interactions: 282070 Sorted by model distance: nonbonded pdb=" O3B ATP Q 600 " pdb="MG MG Q 601 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR Q 64 " pdb="MG MG Q 601 " model vdw 2.052 2.170 nonbonded pdb=" O4 U M 35 " pdb=" N6 A M 36 " model vdw 2.163 2.520 nonbonded pdb=" O4 U M 23 " pdb=" N6 A M 24 " model vdw 2.165 2.520 nonbonded pdb=" OG SER E 28 " pdb=" O GLU E 174 " model vdw 2.211 2.440 ... (remaining 282065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 12.960 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 95.060 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33794 Z= 0.193 Angle : 0.647 10.058 46351 Z= 0.369 Chirality : 0.040 0.227 5011 Planarity : 0.004 0.088 5356 Dihedral : 19.406 179.052 13308 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.59 % Favored : 92.93 % Rotamer: Outliers : 0.72 % Allowed : 20.38 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.06 (0.14), residues: 3552 helix: 1.26 (0.14), residues: 1332 sheet: -0.91 (0.20), residues: 640 loop : -0.72 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP I 63 HIS 0.008 0.001 HIS Q 30 PHE 0.019 0.001 PHE G 234 TYR 0.038 0.001 TYR C 244 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 414 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6431 (tpt) cc_final: 0.6144 (tpt) REVERT: A 116 LEU cc_start: 0.9273 (tp) cc_final: 0.9016 (tp) REVERT: A 166 ASP cc_start: 0.7416 (t0) cc_final: 0.7192 (t0) REVERT: A 202 ASP cc_start: 0.8014 (p0) cc_final: 0.7730 (p0) REVERT: A 209 GLN cc_start: 0.8822 (tt0) cc_final: 0.8542 (mt0) REVERT: B 43 HIS cc_start: 0.8980 (t70) cc_final: 0.8729 (t70) REVERT: B 118 ARG cc_start: 0.5291 (tmt170) cc_final: 0.4265 (ttt-90) REVERT: B 213 ARG cc_start: 0.4448 (tpp80) cc_final: 0.3957 (tpp80) REVERT: C 227 VAL cc_start: 0.9296 (t) cc_final: 0.9057 (p) REVERT: E 256 GLN cc_start: 0.8592 (tp40) cc_final: 0.8300 (tp-100) REVERT: I 358 TRP cc_start: 0.5735 (OUTLIER) cc_final: 0.5470 (p90) REVERT: J 37 LYS cc_start: 0.7961 (pttt) cc_final: 0.7733 (pttp) REVERT: J 87 LEU cc_start: 0.9233 (tp) cc_final: 0.8988 (tp) REVERT: K 5 SER cc_start: 0.8481 (t) cc_final: 0.8213 (p) REVERT: K 20 GLN cc_start: 0.8797 (tp40) cc_final: 0.8421 (tp40) REVERT: P 132 PHE cc_start: 0.7367 (m-80) cc_final: 0.7035 (m-10) REVERT: Q 79 LEU cc_start: 0.7910 (tp) cc_final: 0.7547 (mt) REVERT: Q 95 GLU cc_start: 0.4823 (tt0) cc_final: 0.4519 (pp20) REVERT: Q 124 HIS cc_start: 0.7081 (m-70) cc_final: 0.6790 (m-70) REVERT: Q 164 HIS cc_start: 0.8634 (t-90) cc_final: 0.8340 (t70) REVERT: Q 176 PHE cc_start: 0.6010 (m-80) cc_final: 0.5673 (m-80) REVERT: Q 321 GLU cc_start: 0.4913 (tt0) cc_final: 0.4625 (mm-30) outliers start: 23 outliers final: 6 residues processed: 428 average time/residue: 0.4281 time to fit residues: 294.2505 Evaluate side-chains 292 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 285 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain P residue 110 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 287 optimal weight: 0.0370 chunk 111 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 333 optimal weight: 0.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33794 Z= 0.257 Angle : 0.590 8.592 46351 Z= 0.315 Chirality : 0.040 0.192 5011 Planarity : 0.005 0.089 5356 Dihedral : 19.049 176.066 6017 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.64 % Favored : 92.96 % Rotamer: Outliers : 3.20 % Allowed : 18.93 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.09 (0.14), residues: 3552 helix: 1.21 (0.14), residues: 1331 sheet: -0.99 (0.20), residues: 611 loop : -0.68 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 63 HIS 0.011 0.001 HIS P 48 PHE 0.019 0.001 PHE I 362 TYR 0.018 0.001 TYR P 154 ARG 0.005 0.000 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 281 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6174 (tpt) cc_final: 0.5955 (tpt) REVERT: A 202 ASP cc_start: 0.8246 (p0) cc_final: 0.7817 (p0) REVERT: A 207 MET cc_start: 0.8369 (ttp) cc_final: 0.8163 (ttp) REVERT: A 209 GLN cc_start: 0.8873 (tt0) cc_final: 0.8495 (mt0) REVERT: B 43 HIS cc_start: 0.9019 (t70) cc_final: 0.8777 (t70) REVERT: B 213 ARG cc_start: 0.4553 (tpp80) cc_final: 0.4009 (tpp80) REVERT: F 30 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7734 (m110) REVERT: G 77 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7807 (mtm-85) REVERT: H 250 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7500 (ptmt) REVERT: I 62 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7168 (m-10) REVERT: I 152 PHE cc_start: 0.8323 (t80) cc_final: 0.8030 (t80) REVERT: I 303 MET cc_start: 0.8649 (mmp) cc_final: 0.8079 (mmm) REVERT: I 358 TRP cc_start: 0.5716 (OUTLIER) cc_final: 0.5501 (p90) REVERT: I 451 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8741 (tp30) REVERT: K 5 SER cc_start: 0.8327 (t) cc_final: 0.8110 (p) REVERT: K 20 GLN cc_start: 0.8866 (tp40) cc_final: 0.8449 (tp40) REVERT: L 103 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9165 (mm) REVERT: P 105 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9206 (pp) REVERT: P 132 PHE cc_start: 0.7496 (m-80) cc_final: 0.7187 (m-80) REVERT: P 154 TYR cc_start: 0.8007 (p90) cc_final: 0.7784 (p90) REVERT: P 267 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8320 (t0) REVERT: Q 79 LEU cc_start: 0.8154 (tp) cc_final: 0.7767 (mt) REVERT: Q 95 GLU cc_start: 0.4930 (tt0) cc_final: 0.4605 (pp20) REVERT: Q 156 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6845 (mt) REVERT: Q 176 PHE cc_start: 0.6154 (m-80) cc_final: 0.5760 (m-80) outliers start: 102 outliers final: 45 residues processed: 366 average time/residue: 0.4328 time to fit residues: 260.6814 Evaluate side-chains 312 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 257 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 267 ASP Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 156 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 333 optimal weight: 0.8980 chunk 360 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 331 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 267 optimal weight: 0.4980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 GLN B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN D 176 HIS ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN G 256 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33794 Z= 0.269 Angle : 0.574 8.094 46351 Z= 0.307 Chirality : 0.039 0.201 5011 Planarity : 0.004 0.092 5356 Dihedral : 18.918 174.701 6009 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.67 % Favored : 92.91 % Rotamer: Outliers : 3.77 % Allowed : 18.46 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.05 (0.14), residues: 3552 helix: 1.18 (0.14), residues: 1333 sheet: -0.88 (0.20), residues: 608 loop : -0.65 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 PHE 0.027 0.001 PHE Q 270 TYR 0.019 0.001 TYR G 182 ARG 0.004 0.000 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 274 time to evaluate : 3.943 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 1 MET cc_start: 0.6537 (tpt) cc_final: 0.6326 (tpt) REVERT: A 202 ASP cc_start: 0.8290 (p0) cc_final: 0.7771 (p0) REVERT: A 207 MET cc_start: 0.8509 (ttp) cc_final: 0.8302 (ttp) REVERT: A 209 GLN cc_start: 0.8901 (tt0) cc_final: 0.8495 (mt0) REVERT: B 43 HIS cc_start: 0.9002 (t70) cc_final: 0.8783 (t70) REVERT: B 118 ARG cc_start: 0.4858 (tmt170) cc_final: 0.3787 (mtp180) REVERT: C 244 TYR cc_start: 0.6984 (t80) cc_final: 0.6650 (t80) REVERT: F 30 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.7937 (m-40) REVERT: G 77 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7843 (mtm-85) REVERT: G 108 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8696 (tp) REVERT: H 250 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7551 (ptmt) REVERT: H 293 LEU cc_start: 0.9724 (tp) cc_final: 0.9497 (tt) REVERT: I 62 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7251 (m-10) REVERT: I 152 PHE cc_start: 0.8336 (t80) cc_final: 0.8132 (t80) REVERT: I 303 MET cc_start: 0.8650 (mmp) cc_final: 0.7972 (mmm) REVERT: I 358 TRP cc_start: 0.5759 (OUTLIER) cc_final: 0.5544 (p90) REVERT: I 361 ASN cc_start: 0.6311 (OUTLIER) cc_final: 0.5471 (t0) REVERT: I 396 ASP cc_start: 0.7279 (t0) cc_final: 0.6680 (t0) REVERT: I 451 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8699 (tp30) REVERT: J 20 GLN cc_start: 0.9120 (tp40) cc_final: 0.8756 (tt0) REVERT: K 5 SER cc_start: 0.8395 (t) cc_final: 0.8140 (p) REVERT: K 20 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8581 (tp40) REVERT: L 99 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9222 (mp) REVERT: L 103 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9198 (mm) REVERT: P 40 TYR cc_start: 0.8979 (t80) cc_final: 0.8565 (t80) REVERT: P 105 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9275 (pp) REVERT: P 132 PHE cc_start: 0.7503 (m-80) cc_final: 0.7220 (m-80) REVERT: P 154 TYR cc_start: 0.8133 (p90) cc_final: 0.7856 (p90) REVERT: P 267 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8352 (t0) REVERT: Q 95 GLU cc_start: 0.4906 (tt0) cc_final: 0.4576 (pp20) REVERT: Q 156 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6825 (mt) REVERT: Q 176 PHE cc_start: 0.6113 (m-80) cc_final: 0.5637 (m-80) outliers start: 120 outliers final: 67 residues processed: 368 average time/residue: 0.4209 time to fit residues: 252.6522 Evaluate side-chains 336 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 256 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 281 ASP Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 267 ASP Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 156 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 173 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 335 optimal weight: 0.6980 chunk 354 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 317 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33794 Z= 0.256 Angle : 0.567 9.576 46351 Z= 0.301 Chirality : 0.039 0.205 5011 Planarity : 0.004 0.094 5356 Dihedral : 18.807 173.898 6009 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.81 % Favored : 92.74 % Rotamer: Outliers : 3.74 % Allowed : 19.28 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.13 (0.14), residues: 3552 helix: 1.11 (0.14), residues: 1350 sheet: -0.91 (0.21), residues: 593 loop : -0.72 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 63 HIS 0.008 0.001 HIS I 49 PHE 0.017 0.001 PHE Q 244 TYR 0.018 0.001 TYR L 11 ARG 0.003 0.000 ARG H 302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 273 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6527 (tpt) cc_final: 0.6299 (tpt) REVERT: A 202 ASP cc_start: 0.8254 (p0) cc_final: 0.7736 (p0) REVERT: A 207 MET cc_start: 0.8597 (ttp) cc_final: 0.8370 (ttp) REVERT: C 244 TYR cc_start: 0.7023 (t80) cc_final: 0.6574 (t80) REVERT: F 30 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7815 (m110) REVERT: F 77 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8542 (ttp-170) REVERT: F 136 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6935 (mmm-85) REVERT: F 137 MET cc_start: 0.8315 (tpt) cc_final: 0.8115 (tpt) REVERT: G 77 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7834 (mtm-85) REVERT: G 108 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8669 (tp) REVERT: G 221 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.8079 (t80) REVERT: H 293 LEU cc_start: 0.9718 (tp) cc_final: 0.9487 (tt) REVERT: I 303 MET cc_start: 0.8684 (mmp) cc_final: 0.8096 (mmm) REVERT: I 358 TRP cc_start: 0.5789 (OUTLIER) cc_final: 0.5545 (p90) REVERT: I 396 ASP cc_start: 0.7456 (t0) cc_final: 0.7224 (t70) REVERT: K 5 SER cc_start: 0.8379 (t) cc_final: 0.8130 (p) REVERT: K 20 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8582 (tp40) REVERT: L 99 ILE cc_start: 0.9450 (mp) cc_final: 0.9239 (mp) REVERT: L 103 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9198 (mm) REVERT: P 40 TYR cc_start: 0.8983 (t80) cc_final: 0.8560 (t80) REVERT: P 105 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9297 (pp) REVERT: P 154 TYR cc_start: 0.8173 (p90) cc_final: 0.7902 (p90) REVERT: P 267 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8440 (t0) REVERT: Q 95 GLU cc_start: 0.4851 (tt0) cc_final: 0.4360 (pp20) REVERT: Q 156 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6820 (mt) REVERT: Q 176 PHE cc_start: 0.6062 (m-80) cc_final: 0.5478 (m-80) outliers start: 119 outliers final: 70 residues processed: 367 average time/residue: 0.4063 time to fit residues: 246.2535 Evaluate side-chains 333 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 252 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 281 ASP Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 267 ASP Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 156 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 266 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 295 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 264 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 245 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 318 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 33794 Z= 0.379 Angle : 0.632 10.613 46351 Z= 0.333 Chirality : 0.041 0.215 5011 Planarity : 0.005 0.097 5356 Dihedral : 18.808 173.159 6007 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.29 % Favored : 92.23 % Rotamer: Outliers : 4.18 % Allowed : 20.09 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.22 (0.14), residues: 3552 helix: 1.02 (0.14), residues: 1347 sheet: -1.01 (0.21), residues: 599 loop : -0.72 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 63 HIS 0.008 0.001 HIS B 51 PHE 0.019 0.002 PHE C 221 TYR 0.021 0.002 TYR K 11 ARG 0.004 0.000 ARG H 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 257 time to evaluate : 3.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8372 (p0) cc_final: 0.7982 (p0) REVERT: B 187 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7561 (tm-30) REVERT: C 244 TYR cc_start: 0.7168 (t80) cc_final: 0.6828 (t80) REVERT: F 30 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8477 (t0) REVERT: F 77 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8880 (mtm110) REVERT: F 136 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7045 (mmm-85) REVERT: G 77 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7824 (mtm-85) REVERT: G 108 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8598 (tp) REVERT: G 221 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8102 (t80) REVERT: I 358 TRP cc_start: 0.5809 (OUTLIER) cc_final: 0.5598 (p90) REVERT: I 396 ASP cc_start: 0.7639 (t0) cc_final: 0.7430 (t70) REVERT: J 112 ASP cc_start: 0.6028 (OUTLIER) cc_final: 0.4762 (p0) REVERT: K 5 SER cc_start: 0.8416 (t) cc_final: 0.8139 (p) REVERT: K 20 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8582 (tp40) REVERT: L 95 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8755 (mp10) REVERT: L 103 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9270 (mm) REVERT: P 21 LEU cc_start: 0.9157 (mm) cc_final: 0.8930 (mm) REVERT: P 40 TYR cc_start: 0.9037 (t80) cc_final: 0.8732 (t80) REVERT: P 105 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9309 (pp) REVERT: P 154 TYR cc_start: 0.8315 (p90) cc_final: 0.7969 (p90) REVERT: Q 95 GLU cc_start: 0.4874 (tt0) cc_final: 0.4310 (pp20) outliers start: 133 outliers final: 86 residues processed: 364 average time/residue: 0.4167 time to fit residues: 248.6982 Evaluate side-chains 337 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 240 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 281 ASP Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 266 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 3.9990 chunk 319 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 208 optimal weight: 0.0050 chunk 87 optimal weight: 3.9990 chunk 355 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33794 Z= 0.245 Angle : 0.570 10.817 46351 Z= 0.303 Chirality : 0.039 0.207 5011 Planarity : 0.004 0.098 5356 Dihedral : 18.761 172.778 6007 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.81 % Favored : 92.74 % Rotamer: Outliers : 3.92 % Allowed : 20.66 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.09 (0.15), residues: 3552 helix: 1.12 (0.14), residues: 1347 sheet: -0.87 (0.21), residues: 587 loop : -0.69 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 63 HIS 0.005 0.001 HIS Q 30 PHE 0.019 0.001 PHE F 234 TYR 0.029 0.001 TYR A 37 ARG 0.003 0.000 ARG H 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 269 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6392 (tpt) cc_final: 0.5654 (tpt) REVERT: A 92 TYR cc_start: 0.9056 (m-80) cc_final: 0.8685 (m-80) REVERT: A 202 ASP cc_start: 0.8394 (p0) cc_final: 0.8024 (p0) REVERT: A 209 GLN cc_start: 0.8777 (tt0) cc_final: 0.8523 (mt0) REVERT: B 118 ARG cc_start: 0.4438 (tmt170) cc_final: 0.3396 (mtp180) REVERT: B 187 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 204 MET cc_start: 0.8325 (tpp) cc_final: 0.7959 (tpt) REVERT: C 244 TYR cc_start: 0.7150 (t80) cc_final: 0.6766 (t80) REVERT: D 226 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8901 (mt) REVERT: F 30 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7789 (m110) REVERT: F 77 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8876 (mtm110) REVERT: F 136 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.7008 (mmm-85) REVERT: G 77 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7865 (mtm-85) REVERT: G 108 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8595 (tp) REVERT: G 221 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8039 (t80) REVERT: I 26 MET cc_start: 0.8759 (mmm) cc_final: 0.8142 (mmt) REVERT: I 52 TRP cc_start: 0.7549 (p90) cc_final: 0.7032 (p90) REVERT: I 358 TRP cc_start: 0.5834 (OUTLIER) cc_final: 0.5628 (p90) REVERT: I 361 ASN cc_start: 0.6233 (OUTLIER) cc_final: 0.5366 (t0) REVERT: I 396 ASP cc_start: 0.7614 (t0) cc_final: 0.7395 (t70) REVERT: J 112 ASP cc_start: 0.5931 (OUTLIER) cc_final: 0.4647 (p0) REVERT: K 5 SER cc_start: 0.8386 (t) cc_final: 0.8108 (p) REVERT: K 20 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8553 (tp40) REVERT: L 103 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9229 (mm) REVERT: P 21 LEU cc_start: 0.9135 (mm) cc_final: 0.8910 (mm) REVERT: P 40 TYR cc_start: 0.9017 (t80) cc_final: 0.8746 (t80) REVERT: P 54 LYS cc_start: 0.8444 (mmtt) cc_final: 0.7926 (ttmm) REVERT: P 105 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9303 (pp) REVERT: P 154 TYR cc_start: 0.8238 (p90) cc_final: 0.7945 (p90) REVERT: Q 95 GLU cc_start: 0.4871 (tt0) cc_final: 0.4293 (pp20) outliers start: 125 outliers final: 87 residues processed: 368 average time/residue: 0.4180 time to fit residues: 253.1066 Evaluate side-chains 351 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 252 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 80 HIS Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 124 HIS Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 266 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 342 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 198 optimal weight: 0.0970 chunk 353 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33794 Z= 0.298 Angle : 0.592 10.053 46351 Z= 0.313 Chirality : 0.040 0.215 5011 Planarity : 0.004 0.100 5356 Dihedral : 18.753 172.239 6007 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.95 % Favored : 92.60 % Rotamer: Outliers : 4.08 % Allowed : 20.60 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.10 (0.15), residues: 3552 helix: 1.15 (0.14), residues: 1336 sheet: -0.93 (0.21), residues: 619 loop : -0.67 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 63 HIS 0.023 0.001 HIS Q 124 PHE 0.015 0.001 PHE C 221 TYR 0.023 0.001 TYR A 37 ARG 0.003 0.000 ARG H 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 259 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6488 (tpt) cc_final: 0.5840 (tpt) REVERT: A 202 ASP cc_start: 0.8417 (p0) cc_final: 0.8069 (p0) REVERT: A 209 GLN cc_start: 0.8777 (tt0) cc_final: 0.8510 (mt0) REVERT: B 118 ARG cc_start: 0.4471 (tmt170) cc_final: 0.3362 (mtp180) REVERT: B 187 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 244 TYR cc_start: 0.7194 (t80) cc_final: 0.6822 (t80) REVERT: D 226 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8904 (mt) REVERT: F 77 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8909 (mtm110) REVERT: F 136 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7041 (mmm-85) REVERT: F 268 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8657 (p0) REVERT: G 77 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7860 (mtm-85) REVERT: G 108 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8562 (tp) REVERT: G 181 GLN cc_start: 0.8646 (tt0) cc_final: 0.8336 (tt0) REVERT: G 221 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8060 (t80) REVERT: I 26 MET cc_start: 0.8763 (mmm) cc_final: 0.8146 (mmt) REVERT: I 358 TRP cc_start: 0.5923 (OUTLIER) cc_final: 0.5470 (p90) REVERT: I 361 ASN cc_start: 0.6254 (OUTLIER) cc_final: 0.5382 (t0) REVERT: J 112 ASP cc_start: 0.6018 (OUTLIER) cc_final: 0.4768 (p0) REVERT: K 5 SER cc_start: 0.8386 (t) cc_final: 0.8110 (p) REVERT: K 20 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8567 (tp40) REVERT: L 95 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8782 (mp10) REVERT: L 103 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9261 (mm) REVERT: P 40 TYR cc_start: 0.9007 (t80) cc_final: 0.8752 (t80) REVERT: P 105 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9336 (pp) REVERT: P 147 MET cc_start: 0.6844 (ttp) cc_final: 0.6563 (ptm) REVERT: P 154 TYR cc_start: 0.8285 (p90) cc_final: 0.7964 (p90) REVERT: Q 124 HIS cc_start: 0.6834 (m-70) cc_final: 0.6583 (m90) REVERT: Q 156 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6874 (mt) outliers start: 130 outliers final: 100 residues processed: 364 average time/residue: 0.4221 time to fit residues: 255.1468 Evaluate side-chains 358 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 244 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 410 MET Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 80 HIS Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 282 ASN Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 156 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 266 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 218 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 211 optimal weight: 0.0270 chunk 106 optimal weight: 0.0870 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 278 optimal weight: 0.4980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 ASN E 42 GLN F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN H 13 ASN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 33794 Z= 0.157 Angle : 0.554 11.960 46351 Z= 0.293 Chirality : 0.039 0.195 5011 Planarity : 0.004 0.099 5356 Dihedral : 18.681 172.851 6007 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.17 % Favored : 93.47 % Rotamer: Outliers : 2.83 % Allowed : 21.95 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3552 helix: 1.16 (0.14), residues: 1351 sheet: -0.87 (0.21), residues: 632 loop : -0.59 (0.17), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 PHE 0.027 0.001 PHE F 234 TYR 0.021 0.001 TYR G 182 ARG 0.004 0.000 ARG P 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 289 time to evaluate : 4.018 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 1 MET cc_start: 0.6518 (tpt) cc_final: 0.5853 (tpt) REVERT: A 202 ASP cc_start: 0.8386 (p0) cc_final: 0.8017 (p0) REVERT: B 118 ARG cc_start: 0.4363 (tmt170) cc_final: 0.3731 (ttt-90) REVERT: B 187 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7420 (tm-30) REVERT: D 77 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8245 (ttp-170) REVERT: D 226 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8861 (mt) REVERT: E 137 MET cc_start: 0.8943 (tpp) cc_final: 0.8711 (tpp) REVERT: E 247 PRO cc_start: 0.7583 (Cg_exo) cc_final: 0.7343 (Cg_endo) REVERT: F 30 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7653 (m110) REVERT: F 77 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8776 (ttp80) REVERT: F 268 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8560 (p0) REVERT: F 282 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8937 (mm) REVERT: G 221 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.7978 (t80) REVERT: H 302 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8621 (mtt90) REVERT: I 26 MET cc_start: 0.8627 (mmm) cc_final: 0.8021 (mmt) REVERT: I 222 LYS cc_start: 0.8188 (tptp) cc_final: 0.7788 (mmmt) REVERT: I 306 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8020 (tm-30) REVERT: I 358 TRP cc_start: 0.5812 (OUTLIER) cc_final: 0.5370 (p90) REVERT: I 451 GLU cc_start: 0.9077 (tp30) cc_final: 0.8657 (tp30) REVERT: J 112 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.4668 (p0) REVERT: K 5 SER cc_start: 0.8277 (t) cc_final: 0.7997 (p) REVERT: K 20 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8512 (tp40) REVERT: L 95 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8727 (mp10) REVERT: L 103 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9203 (mm) REVERT: P 40 TYR cc_start: 0.8959 (t80) cc_final: 0.8700 (t80) REVERT: P 99 GLU cc_start: 0.9291 (tp30) cc_final: 0.9004 (tm-30) REVERT: P 105 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9310 (pp) REVERT: Q 54 PHE cc_start: 0.4557 (m-10) cc_final: 0.3995 (m-10) REVERT: Q 124 HIS cc_start: 0.6822 (m-70) cc_final: 0.6495 (m90) REVERT: Q 156 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6887 (mt) REVERT: Q 318 MET cc_start: 0.3519 (ptt) cc_final: 0.3014 (tmm) outliers start: 90 outliers final: 58 residues processed: 356 average time/residue: 0.4122 time to fit residues: 243.2339 Evaluate side-chains 338 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 266 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 55 CYS Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 80 HIS Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain Q residue 156 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 266 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 7.9990 chunk 338 optimal weight: 20.0000 chunk 309 optimal weight: 2.9990 chunk 329 optimal weight: 4.9990 chunk 198 optimal weight: 0.0270 chunk 143 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 101 optimal weight: 0.2980 chunk 297 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 328 optimal weight: 2.9990 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 GLN ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33794 Z= 0.259 Angle : 0.584 10.801 46351 Z= 0.309 Chirality : 0.039 0.199 5011 Planarity : 0.004 0.100 5356 Dihedral : 18.652 171.309 6007 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.78 % Favored : 92.79 % Rotamer: Outliers : 2.64 % Allowed : 22.54 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.00 (0.15), residues: 3552 helix: 1.24 (0.14), residues: 1338 sheet: -0.90 (0.21), residues: 620 loop : -0.60 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 63 HIS 0.005 0.001 HIS Q 30 PHE 0.012 0.001 PHE C 221 TYR 0.022 0.001 TYR A 37 ARG 0.003 0.000 ARG H 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 265 time to evaluate : 3.602 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 1 MET cc_start: 0.6608 (tpt) cc_final: 0.6008 (tpt) REVERT: A 202 ASP cc_start: 0.8408 (p0) cc_final: 0.8067 (p0) REVERT: B 118 ARG cc_start: 0.4332 (tmt170) cc_final: 0.3642 (ttt-90) REVERT: B 187 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7488 (tm-30) REVERT: D 77 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8472 (ttp-170) REVERT: D 226 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8875 (mt) REVERT: F 30 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7984 (m-40) REVERT: F 77 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8890 (mtm110) REVERT: F 234 PHE cc_start: 0.7909 (t80) cc_final: 0.7635 (t80) REVERT: F 268 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8563 (p0) REVERT: G 221 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.7961 (t80) REVERT: I 26 MET cc_start: 0.8691 (mmm) cc_final: 0.8072 (mmt) REVERT: I 62 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: I 222 LYS cc_start: 0.8188 (tptp) cc_final: 0.7983 (mmmt) REVERT: I 358 TRP cc_start: 0.5962 (OUTLIER) cc_final: 0.5420 (p90) REVERT: I 451 GLU cc_start: 0.9092 (tp30) cc_final: 0.8580 (tp30) REVERT: J 112 ASP cc_start: 0.5869 (OUTLIER) cc_final: 0.4596 (p0) REVERT: K 5 SER cc_start: 0.8309 (t) cc_final: 0.8069 (p) REVERT: K 20 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8572 (tp40) REVERT: L 95 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8801 (mp10) REVERT: L 103 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9256 (mm) REVERT: P 99 GLU cc_start: 0.9282 (tp30) cc_final: 0.9015 (tm-30) REVERT: P 114 LEU cc_start: 0.9229 (mm) cc_final: 0.9013 (tt) REVERT: Q 54 PHE cc_start: 0.4383 (m-10) cc_final: 0.4107 (m-10) REVERT: Q 124 HIS cc_start: 0.6838 (m-70) cc_final: 0.6456 (m90) REVERT: Q 156 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6806 (mt) REVERT: Q 164 HIS cc_start: 0.8740 (t70) cc_final: 0.8190 (t70) REVERT: Q 318 MET cc_start: 0.3940 (ptt) cc_final: 0.3505 (tmm) outliers start: 84 outliers final: 57 residues processed: 328 average time/residue: 0.4060 time to fit residues: 221.0917 Evaluate side-chains 324 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 255 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 80 HIS Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain Q residue 156 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 266 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 10.0000 chunk 348 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 365 optimal weight: 20.0000 chunk 336 optimal weight: 0.2980 chunk 291 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN F 181 GLN G 48 ASN G 181 GLN H 13 ASN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33794 Z= 0.189 Angle : 0.570 12.477 46351 Z= 0.301 Chirality : 0.039 0.209 5011 Planarity : 0.004 0.101 5356 Dihedral : 18.628 172.187 6007 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.59 % Favored : 93.05 % Rotamer: Outliers : 2.39 % Allowed : 22.95 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.03 (0.15), residues: 3552 helix: 1.22 (0.14), residues: 1342 sheet: -0.79 (0.21), residues: 623 loop : -0.60 (0.17), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 63 HIS 0.005 0.001 HIS Q 30 PHE 0.042 0.001 PHE G 234 TYR 0.025 0.001 TYR C 244 ARG 0.003 0.000 ARG B 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 270 time to evaluate : 3.546 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 1 MET cc_start: 0.6557 (tpt) cc_final: 0.5979 (tpt) REVERT: A 202 ASP cc_start: 0.8410 (p0) cc_final: 0.8075 (p0) REVERT: B 118 ARG cc_start: 0.4498 (tmt170) cc_final: 0.3691 (mtp180) REVERT: B 187 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7498 (tm-30) REVERT: C 244 TYR cc_start: 0.7116 (t80) cc_final: 0.6809 (t80) REVERT: D 77 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8376 (ttp-170) REVERT: D 144 MET cc_start: 0.9068 (ttp) cc_final: 0.8682 (ttp) REVERT: D 226 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8895 (mt) REVERT: E 137 MET cc_start: 0.8949 (tpp) cc_final: 0.8731 (tpp) REVERT: F 30 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7670 (m110) REVERT: F 77 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8861 (mtm110) REVERT: F 234 PHE cc_start: 0.7932 (t80) cc_final: 0.7679 (t80) REVERT: F 268 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8586 (p0) REVERT: G 221 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8031 (t80) REVERT: I 26 MET cc_start: 0.8653 (mmm) cc_final: 0.8044 (mmt) REVERT: I 291 GLU cc_start: 0.8239 (tt0) cc_final: 0.7985 (pt0) REVERT: I 451 GLU cc_start: 0.9070 (tp30) cc_final: 0.8621 (tp30) REVERT: J 112 ASP cc_start: 0.5877 (OUTLIER) cc_final: 0.4676 (p0) REVERT: K 5 SER cc_start: 0.8290 (t) cc_final: 0.8033 (p) REVERT: K 20 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8542 (tp40) REVERT: L 95 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8745 (mp10) REVERT: L 103 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9209 (mm) REVERT: P 99 GLU cc_start: 0.9257 (tp30) cc_final: 0.9031 (tm-30) REVERT: P 114 LEU cc_start: 0.9246 (mm) cc_final: 0.9021 (tt) REVERT: Q 124 HIS cc_start: 0.6836 (m-70) cc_final: 0.6527 (m90) REVERT: Q 156 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6851 (mt) REVERT: Q 164 HIS cc_start: 0.8766 (t70) cc_final: 0.8235 (t70) REVERT: Q 318 MET cc_start: 0.4100 (ptt) cc_final: 0.3653 (tmm) outliers start: 76 outliers final: 53 residues processed: 329 average time/residue: 0.4087 time to fit residues: 223.3220 Evaluate side-chains 322 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 259 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain P residue 80 HIS Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain Q residue 156 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 266 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 268 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 ASN ** I 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.104015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.068687 restraints weight = 94126.075| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.78 r_work: 0.2907 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33794 Z= 0.349 Angle : 0.642 24.552 46351 Z= 0.333 Chirality : 0.041 0.262 5011 Planarity : 0.005 0.184 5356 Dihedral : 18.614 170.254 6002 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.40 % Favored : 92.15 % Rotamer: Outliers : 2.67 % Allowed : 22.79 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.05 (0.15), residues: 3552 helix: 1.16 (0.15), residues: 1336 sheet: -0.83 (0.21), residues: 621 loop : -0.65 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 63 HIS 0.006 0.001 HIS B 51 PHE 0.018 0.001 PHE C 221 TYR 0.030 0.002 TYR A 37 ARG 0.006 0.000 ARG F 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7378.18 seconds wall clock time: 134 minutes 39.44 seconds (8079.44 seconds total)