Starting phenix.real_space_refine on Tue Feb 20 03:17:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd3_29001/02_2024/8fd3_29001.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd3_29001/02_2024/8fd3_29001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd3_29001/02_2024/8fd3_29001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd3_29001/02_2024/8fd3_29001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd3_29001/02_2024/8fd3_29001.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd3_29001/02_2024/8fd3_29001.pdb" } resolution = 3.12 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= 0.013 sd= 0.034 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 408 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: 5 Type Number sf(0) Gaussians P 85 5.49 5 S 94 5.16 5 C 16536 2.51 5 N 4460 2.21 5 O 5075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F GLU 251": "OE1" <-> "OE2" Residue "G GLU 257": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26250 Number of models: 1 Model: "" Number of chains: 15 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: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1727 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 202} 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: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2345 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} 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: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2351 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "H" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2420 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} 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': 15, 'rna2p_pyr': 10, 'rna3p_pur': 18, 'rna3p_pyr': 20} Link IDs: {'rna2p': 25, 'rna3p': 37} Chain: "N" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "O" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 13.66, per 1000 atoms: 0.52 Number of scatterers: 26250 At special positions: 0 Unit cell: (101.184, 115.94, 198.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 85 15.00 O 5075 8.00 N 4460 7.00 C 16536 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: 11.52 Conformation dependent library (CDL) restraints added in 4.8 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5590 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 51 sheets defined 39.4% alpha, 23.4% beta 12 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 9.61 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.584A pdb=" N TRP A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 40 through 45 removed outlier: 4.325A pdb=" N GLU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.817A pdb=" N MET B 204 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.618A pdb=" N THR B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) 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 56 through 71 removed outlier: 3.729A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 196 through 206 removed outlier: 3.572A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.645A pdb=" N SER C 214 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.552A pdb=" N GLY C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.661A pdb=" N ASP C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 318 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 56 through 71 removed outlier: 3.576A pdb=" N ILE D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.522A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.784A pdb=" N GLY D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.084A pdb=" N ASP D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.598A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.521A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.883A pdb=" N GLY E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 277 through 284 removed outlier: 4.092A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 301 through 318 Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.643A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.772A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.826A pdb=" N GLY F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.957A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 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 56 through 71 removed outlier: 3.748A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 206 removed outlier: 3.644A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 277 through 284 removed outlier: 4.009A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 318 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 56 through 71 removed outlier: 3.531A pdb=" N ILE H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 109 through 112 Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 206 removed outlier: 3.573A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.679A pdb=" N GLY H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 270 No H-bonds generated for 'chain 'H' and resid 268 through 270' Processing helix chain 'H' and resid 277 through 285 removed outlier: 3.921A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.604A pdb=" N LYS H 295 " --> pdb=" O PRO H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 317 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.747A pdb=" N ILE I 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.585A pdb=" N ALA I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 116 through 118 No H-bonds generated for 'chain 'I' and resid 116 through 118' Processing helix chain 'I' and resid 148 through 157 removed outlier: 5.400A pdb=" N ALA I 153 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 removed outlier: 3.505A pdb=" N GLN I 187 " --> pdb=" O ALA I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 251 through 252 No H-bonds generated for 'chain 'I' and resid 251 through 252' Processing helix chain 'I' and resid 253 through 256 Processing helix chain 'I' and resid 261 through 270 removed outlier: 3.502A pdb=" N ALA I 265 " --> pdb=" O SER I 261 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR I 270 " --> pdb=" O GLY I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 Processing helix chain 'I' and resid 361 through 367 removed outlier: 3.668A pdb=" N LYS I 365 " --> pdb=" O ASN I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 382 removed outlier: 4.030A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU I 379 " --> pdb=" O LEU I 375 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE I 380 " --> pdb=" O PHE I 376 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER I 381 " --> pdb=" O ASN I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 392 Processing helix chain 'I' and resid 397 through 421 removed outlier: 3.686A pdb=" N ILE I 417 " --> pdb=" O ASN I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 removed outlier: 3.834A pdb=" N LYS I 432 " --> pdb=" O PRO I 428 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS I 443 " --> pdb=" O GLU I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 460 Processing helix chain 'I' and resid 463 through 469 Processing helix chain 'I' and resid 469 through 480 Processing helix chain 'I' and resid 481 through 495 Processing helix chain 'J' and resid 6 through 33 Processing helix chain 'J' and resid 41 through 53 Processing helix chain 'J' and resid 58 through 72 removed outlier: 5.964A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 removed outlier: 3.716A pdb=" N ILE J 85 " --> pdb=" O HIS J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 107 Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.526A pdb=" N LYS J 111 " --> pdb=" O TYR J 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 removed outlier: 3.817A pdb=" N VAL K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 73 removed outlier: 3.604A pdb=" N GLY K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 93 through 107 Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.768A pdb=" N CYS L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.805A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 Processing helix chain 'L' and resid 81 through 92 Processing helix chain 'L' and resid 93 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.913A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.522A pdb=" N LEU A 57 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N ARG A 165 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 6.588A pdb=" N PHE A 13 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER A 97 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.025A pdb=" N ARG B 19 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 100 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.358A pdb=" N LEU B 109 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N GLU B 10 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N LYS B 107 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N VAL B 12 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N ASP B 105 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 removed outlier: 5.582A pdb=" N VAL B 179 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG B 118 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 181 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR B 116 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.659A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.659A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR C 180 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 15 " --> pdb=" O TRP C 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP C 230 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR C 17 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE C 228 " --> pdb=" O TYR C 17 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 19 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 226 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 21 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.661A pdb=" N GLY C 25 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 155 through 160 removed outlier: 3.545A pdb=" N SER C 169 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR D 180 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.541A pdb=" N GLY D 25 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.996A pdb=" N THR D 39 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AC2, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 244 Processing sheet with id=AC4, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'E' and resid 106 through 107 Processing sheet with id=AC9, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AD1, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.531A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD6, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.520A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.520A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY G 276 " --> pdb=" O TYR G 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AE1, first strand: chain 'G' and resid 77 through 80 removed outlier: 3.633A pdb=" N ILE G 85 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 106 through 107 removed outlier: 3.673A pdb=" N PHE G 106 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AE4, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR H 15 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP H 230 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE7, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AE8, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE9, first strand: chain 'H' and resid 105 through 107 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.569A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AF3, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.476A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AF5, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.255A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 329 through 333 1110 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 10.53 Time building geometry restraints manager: 12.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7329 1.33 - 1.45: 5312 1.45 - 1.57: 14112 1.57 - 1.69: 167 1.69 - 1.81: 149 Bond restraints: 27069 Sorted by residual: bond pdb=" C1' DA O 12 " pdb=" N9 DA O 12 " ideal model delta sigma weight residual 1.460 1.403 0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" CA SER F 28 " pdb=" C SER F 28 " ideal model delta sigma weight residual 1.532 1.502 0.030 1.41e-02 5.03e+03 4.62e+00 bond pdb=" CA SER E 28 " pdb=" C SER E 28 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.61e-02 3.86e+03 2.33e+00 bond pdb=" CA LYS G 250 " pdb=" CB LYS G 250 " ideal model delta sigma weight residual 1.526 1.553 -0.027 1.76e-02 3.23e+03 2.27e+00 bond pdb=" O5' U M 34 " pdb=" C5' U M 34 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 1.91e+00 ... (remaining 27064 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.49: 1165 106.49 - 113.39: 14177 113.39 - 120.28: 9880 120.28 - 127.18: 11271 127.18 - 134.08: 457 Bond angle restraints: 36950 Sorted by residual: angle pdb=" N SER E 28 " pdb=" CA SER E 28 " pdb=" C SER E 28 " ideal model delta sigma weight residual 110.44 103.41 7.03 1.20e+00 6.94e-01 3.43e+01 angle pdb=" N LEU E 29 " pdb=" CA LEU E 29 " pdb=" C LEU E 29 " ideal model delta sigma weight residual 111.03 117.42 -6.39 1.11e+00 8.12e-01 3.31e+01 angle pdb=" N TYR H 244 " pdb=" CA TYR H 244 " pdb=" C TYR H 244 " ideal model delta sigma weight residual 114.56 108.27 6.29 1.27e+00 6.20e-01 2.45e+01 angle pdb=" C ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta sigma weight residual 117.23 111.04 6.19 1.36e+00 5.41e-01 2.07e+01 angle pdb=" N LEU A 198 " pdb=" CA LEU A 198 " pdb=" C LEU A 198 " ideal model delta sigma weight residual 111.40 106.13 5.27 1.22e+00 6.72e-01 1.86e+01 ... (remaining 36945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 15374 35.84 - 71.68: 737 71.68 - 107.52: 42 107.52 - 143.37: 1 143.37 - 179.21: 5 Dihedral angle restraints: 16159 sinusoidal: 7434 harmonic: 8725 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 44.62 155.38 1 1.50e+01 4.44e-03 8.15e+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 73.27 126.73 1 1.50e+01 4.44e-03 6.82e+01 dihedral pdb=" O4' C M 50 " pdb=" C1' C M 50 " pdb=" N1 C M 50 " pdb=" C2 C M 50 " ideal model delta sinusoidal sigma weight residual -128.00 51.21 -179.21 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2852 0.036 - 0.073: 779 0.073 - 0.109: 255 0.109 - 0.146: 59 0.146 - 0.182: 12 Chirality restraints: 3957 Sorted by residual: chirality pdb=" CA PRO F 247 " pdb=" N PRO F 247 " pdb=" C PRO F 247 " pdb=" CB PRO F 247 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA TYR I 334 " pdb=" N TYR I 334 " pdb=" C TYR I 334 " pdb=" CB TYR I 334 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" C1' U M 20 " pdb=" O4' U M 20 " pdb=" C2' U M 20 " pdb=" N1 U M 20 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 3954 not shown) Planarity restraints: 4421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " 0.060 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO F 247 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C PHE J 61 " -0.064 2.00e-02 2.50e+03 pdb=" O PHE J 61 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS J 62 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 209 " 0.042 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO B 210 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " 0.036 5.00e-02 4.00e+02 ... (remaining 4418 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 823 2.69 - 3.24: 25236 3.24 - 3.79: 43362 3.79 - 4.35: 59913 4.35 - 4.90: 96751 Nonbonded interactions: 226085 Sorted by model distance: nonbonded pdb=" O LEU B 184 " pdb=" ND2 ASN B 185 " model vdw 2.137 2.520 nonbonded pdb=" N GLU G 257 " pdb=" OE1 GLU G 257 " model vdw 2.194 2.520 nonbonded pdb=" OG1 THR A 15 " pdb=" NE2 GLN A 143 " model vdw 2.202 2.520 nonbonded pdb=" N GLU J 83 " pdb=" OE1 GLU J 83 " model vdw 2.206 2.520 nonbonded pdb=" OG1 THR E 19 " pdb=" O SER E 239 " model vdw 2.220 2.440 ... (remaining 226080 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' and (resid 12 through 109 or resid 133 through 319)) selection = (chain 'H' and (resid 12 through 109 or resid 133 through 319)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.830 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: 5.240 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 79.700 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 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 0.057 27069 Z= 0.176 Angle : 0.571 11.822 36950 Z= 0.310 Chirality : 0.040 0.182 3957 Planarity : 0.004 0.092 4421 Dihedral : 18.479 179.206 10569 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.40 % Favored : 94.29 % Rotamer: Outliers : 2.76 % Allowed : 20.76 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.44 (0.16), residues: 2943 helix: 1.67 (0.17), residues: 1013 sheet: -0.65 (0.22), residues: 596 loop : -0.22 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 488 HIS 0.004 0.001 HIS I 106 PHE 0.016 0.001 PHE J 26 TYR 0.020 0.001 TYR I 334 ARG 0.009 0.000 ARG I 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 457 time to evaluate : 3.174 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 39 MET cc_start: 0.5729 (tmm) cc_final: 0.5497 (tmm) REVERT: B 204 MET cc_start: 0.6695 (mtp) cc_final: 0.6236 (ptt) REVERT: C 42 GLN cc_start: 0.6925 (tt0) cc_final: 0.6538 (tt0) REVERT: C 71 GLN cc_start: 0.8218 (tp40) cc_final: 0.7780 (mm110) REVERT: C 84 HIS cc_start: 0.6689 (m90) cc_final: 0.5936 (t70) REVERT: D 134 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7793 (p0) REVERT: D 142 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7684 (ttp) REVERT: E 108 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6776 (tt) REVERT: E 305 MET cc_start: 0.7683 (ttp) cc_final: 0.7458 (ttt) REVERT: F 15 TYR cc_start: 0.7257 (m-80) cc_final: 0.6847 (m-80) REVERT: F 29 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6564 (mt) REVERT: F 187 ASP cc_start: 0.7583 (t0) cc_final: 0.7359 (t70) REVERT: G 78 VAL cc_start: 0.8948 (t) cc_final: 0.8716 (m) REVERT: G 137 MET cc_start: 0.7318 (tmm) cc_final: 0.6682 (tmm) REVERT: H 45 TYR cc_start: 0.6114 (m-80) cc_final: 0.5886 (m-80) REVERT: I 157 CYS cc_start: 0.3626 (m) cc_final: 0.2823 (m) REVERT: I 347 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3671 (mt) REVERT: I 382 ASN cc_start: 0.3665 (m-40) cc_final: 0.3123 (m-40) REVERT: J 52 LEU cc_start: 0.8653 (mt) cc_final: 0.8417 (mm) REVERT: L 102 LEU cc_start: 0.7780 (mt) cc_final: 0.7550 (mt) outliers start: 73 outliers final: 20 residues processed: 515 average time/residue: 0.4247 time to fit residues: 331.9109 Evaluate side-chains 259 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 234 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain J residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 93 GLN C 13 ASN C 47 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN D 13 ASN ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN E 229 GLN E 283 GLN F 30 ASN F 31 HIS F 76 ASN F 171 HIS F 181 GLN F 256 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 283 GLN H 13 ASN H 30 ASN H 84 HIS H 134 ASN H 256 GLN I 227 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 27069 Z= 0.455 Angle : 0.761 22.784 36950 Z= 0.397 Chirality : 0.048 0.265 3957 Planarity : 0.006 0.079 4421 Dihedral : 16.887 177.031 4551 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.64 % Favored : 93.99 % Rotamer: Outliers : 4.73 % Allowed : 18.94 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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 (0.16), residues: 2943 helix: 0.87 (0.16), residues: 1027 sheet: -0.73 (0.22), residues: 577 loop : -0.43 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 176 HIS 0.008 0.002 HIS H 52 PHE 0.019 0.002 PHE L 68 TYR 0.031 0.002 TYR K 11 ARG 0.009 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 246 time to evaluate : 3.121 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 196 ASP cc_start: 0.4591 (OUTLIER) cc_final: 0.4099 (t0) REVERT: B 113 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5558 (tm-30) REVERT: B 204 MET cc_start: 0.6407 (mtp) cc_final: 0.6132 (mtm) REVERT: C 261 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: D 34 ARG cc_start: 0.6210 (mtt180) cc_final: 0.5999 (mtt180) REVERT: D 261 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: E 34 ARG cc_start: 0.7012 (mmm-85) cc_final: 0.6706 (mmm160) REVERT: E 64 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8221 (tt) REVERT: E 305 MET cc_start: 0.8165 (ttp) cc_final: 0.7811 (ttt) REVERT: F 15 TYR cc_start: 0.7898 (m-80) cc_final: 0.7255 (m-80) REVERT: F 42 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6595 (tt0) REVERT: F 77 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8109 (mtm180) REVERT: G 33 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7420 (mp) REVERT: G 137 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7270 (tmm) REVERT: G 305 MET cc_start: 0.8359 (ttp) cc_final: 0.8111 (ttp) REVERT: H 14 TYR cc_start: 0.7804 (m-80) cc_final: 0.7294 (m-80) REVERT: H 40 ILE cc_start: 0.8522 (mm) cc_final: 0.8232 (mm) REVERT: H 51 ILE cc_start: 0.8693 (mt) cc_final: 0.8459 (tt) REVERT: H 77 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8015 (mtp180) REVERT: H 87 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8272 (ttm-80) REVERT: H 115 GLU cc_start: 0.5287 (mm-30) cc_final: 0.4927 (tt0) REVERT: H 251 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7598 (mt-10) REVERT: H 283 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: I 139 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.5969 (t80) REVERT: I 157 CYS cc_start: 0.3903 (m) cc_final: 0.3354 (m) REVERT: I 203 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7158 (mt) REVERT: I 382 ASN cc_start: 0.4976 (m-40) cc_final: 0.4589 (m-40) REVERT: I 442 TYR cc_start: 0.6423 (t80) cc_final: 0.5845 (t80) REVERT: J 47 ARG cc_start: 0.8591 (ttm110) cc_final: 0.7924 (ttm110) REVERT: K 7 GLU cc_start: 0.6691 (pm20) cc_final: 0.6215 (pm20) REVERT: K 95 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: K 96 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7915 (mm-30) outliers start: 125 outliers final: 42 residues processed: 356 average time/residue: 0.4125 time to fit residues: 224.9689 Evaluate side-chains 261 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 205 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 217 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 284 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN E 256 GLN E 283 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN G 13 ASN G 42 GLN G 135 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27069 Z= 0.319 Angle : 0.621 16.340 36950 Z= 0.325 Chirality : 0.043 0.243 3957 Planarity : 0.005 0.081 4421 Dihedral : 16.616 177.890 4525 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.30 % Favored : 94.43 % Rotamer: Outliers : 3.40 % Allowed : 19.58 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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 (0.16), residues: 2943 helix: 1.07 (0.16), residues: 1031 sheet: -0.86 (0.22), residues: 556 loop : -0.48 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 176 HIS 0.004 0.001 HIS F 31 PHE 0.022 0.002 PHE C 288 TYR 0.029 0.002 TYR F 244 ARG 0.010 0.001 ARG F 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 225 time to evaluate : 6.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.4498 (OUTLIER) cc_final: 0.4109 (t0) REVERT: B 208 PHE cc_start: 0.6178 (m-80) cc_final: 0.5966 (m-80) REVERT: C 221 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: C 261 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: D 142 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8024 (ttp) REVERT: E 34 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.7011 (mmm160) REVERT: E 305 MET cc_start: 0.8258 (ttp) cc_final: 0.7869 (ttt) REVERT: F 40 ILE cc_start: 0.8275 (mm) cc_final: 0.8039 (mp) REVERT: F 42 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: F 64 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7444 (mt) REVERT: F 83 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7849 (mp0) REVERT: F 244 TYR cc_start: 0.5503 (p90) cc_final: 0.5299 (p90) REVERT: H 14 TYR cc_start: 0.7790 (m-80) cc_final: 0.7556 (m-80) REVERT: H 40 ILE cc_start: 0.8892 (mm) cc_final: 0.8668 (mm) REVERT: H 77 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8218 (ttm-80) REVERT: H 113 GLU cc_start: 0.7743 (pp20) cc_final: 0.7262 (pp20) REVERT: H 240 TYR cc_start: 0.7419 (m-80) cc_final: 0.7189 (m-80) REVERT: H 244 TYR cc_start: 0.7092 (t80) cc_final: 0.6386 (t80) REVERT: H 248 LYS cc_start: 0.8389 (mptt) cc_final: 0.8052 (mptt) REVERT: H 283 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: I 139 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.6226 (t80) REVERT: I 382 ASN cc_start: 0.4549 (m-40) cc_final: 0.4180 (m-40) REVERT: J 47 ARG cc_start: 0.8492 (ttm110) cc_final: 0.8104 (ttm110) REVERT: J 57 ASP cc_start: 0.5894 (t0) cc_final: 0.5683 (t0) REVERT: K 57 ASP cc_start: 0.7129 (t0) cc_final: 0.6909 (t0) REVERT: K 95 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: K 98 ARG cc_start: 0.8664 (ttp-170) cc_final: 0.8373 (ttp80) REVERT: L 47 ARG cc_start: 0.6685 (mmp-170) cc_final: 0.6452 (ttm110) outliers start: 90 outliers final: 41 residues processed: 300 average time/residue: 0.4006 time to fit residues: 192.6918 Evaluate side-chains 243 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 284 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN F 294 ASN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27069 Z= 0.241 Angle : 0.576 15.403 36950 Z= 0.300 Chirality : 0.041 0.219 3957 Planarity : 0.004 0.084 4421 Dihedral : 16.391 177.719 4518 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.64 % Favored : 94.05 % Rotamer: Outliers : 3.48 % Allowed : 19.74 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.08 (0.16), residues: 2943 helix: 1.21 (0.16), residues: 1026 sheet: -0.73 (0.23), residues: 538 loop : -0.40 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 488 HIS 0.006 0.001 HIS E 31 PHE 0.032 0.001 PHE I 53 TYR 0.021 0.001 TYR E 182 ARG 0.005 0.000 ARG I 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 210 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 HIS cc_start: 0.7695 (t70) cc_final: 0.7480 (t-90) REVERT: B 90 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: B 204 MET cc_start: 0.6530 (mtm) cc_final: 0.6047 (mtp) REVERT: C 261 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: E 20 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8218 (p) REVERT: E 137 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: E 305 MET cc_start: 0.8242 (ttp) cc_final: 0.7948 (ttt) REVERT: F 42 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6539 (tt0) REVERT: F 83 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7947 (mp0) REVERT: G 30 ASN cc_start: 0.6174 (OUTLIER) cc_final: 0.5858 (p0) REVERT: H 14 TYR cc_start: 0.7780 (m-80) cc_final: 0.7508 (m-80) REVERT: H 40 ILE cc_start: 0.8880 (mm) cc_final: 0.8649 (mm) REVERT: H 77 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8190 (ttm-80) REVERT: H 113 GLU cc_start: 0.7733 (pp20) cc_final: 0.7308 (pp20) REVERT: H 248 LYS cc_start: 0.8376 (mptt) cc_final: 0.8000 (mptt) REVERT: H 283 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: I 139 TYR cc_start: 0.6626 (OUTLIER) cc_final: 0.6245 (t80) REVERT: I 229 TYR cc_start: 0.3232 (m-10) cc_final: 0.2977 (m-10) REVERT: I 256 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6668 (tp40) REVERT: I 382 ASN cc_start: 0.4451 (m-40) cc_final: 0.4069 (m-40) REVERT: J 57 ASP cc_start: 0.6042 (t0) cc_final: 0.5810 (t0) REVERT: J 95 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.6944 (mp10) REVERT: K 71 ARG cc_start: 0.8492 (mtp85) cc_final: 0.7860 (mtm-85) REVERT: K 95 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: K 98 ARG cc_start: 0.8655 (ttp-170) cc_final: 0.8290 (ttp80) outliers start: 92 outliers final: 51 residues processed: 286 average time/residue: 0.3827 time to fit residues: 175.9381 Evaluate side-chains 255 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 192 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 256 GLN Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 214 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 245 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS I 256 GLN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27069 Z= 0.296 Angle : 0.595 15.930 36950 Z= 0.309 Chirality : 0.042 0.233 3957 Planarity : 0.004 0.085 4421 Dihedral : 16.357 175.250 4514 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.78 % Favored : 93.95 % Rotamer: Outliers : 3.52 % Allowed : 19.85 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 (0.16), residues: 2943 helix: 1.16 (0.16), residues: 1027 sheet: -0.72 (0.23), residues: 545 loop : -0.42 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 488 HIS 0.008 0.001 HIS I 258 PHE 0.018 0.002 PHE A 82 TYR 0.028 0.002 TYR F 244 ARG 0.010 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 198 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.4782 (OUTLIER) cc_final: 0.4503 (t0) REVERT: B 27 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7270 (p0) REVERT: B 43 HIS cc_start: 0.7688 (t70) cc_final: 0.7481 (t-90) REVERT: B 77 HIS cc_start: 0.7703 (p90) cc_final: 0.7148 (p-80) REVERT: B 204 MET cc_start: 0.6786 (mtm) cc_final: 0.6573 (mtp) REVERT: C 144 MET cc_start: 0.8283 (mtp) cc_final: 0.8035 (mtp) REVERT: C 221 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: C 261 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: D 142 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7941 (ttp) REVERT: E 20 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8277 (p) REVERT: E 137 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7463 (tmm) REVERT: E 181 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8242 (pt0) REVERT: E 305 MET cc_start: 0.8261 (ttp) cc_final: 0.7858 (ttt) REVERT: F 42 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: F 64 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7428 (mt) REVERT: F 83 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7982 (mp0) REVERT: H 14 TYR cc_start: 0.7793 (m-80) cc_final: 0.7502 (m-80) REVERT: H 40 ILE cc_start: 0.8964 (mm) cc_final: 0.8756 (mm) REVERT: H 77 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8195 (ttm-80) REVERT: H 113 GLU cc_start: 0.7730 (pp20) cc_final: 0.7360 (pp20) REVERT: H 248 LYS cc_start: 0.8377 (mptt) cc_final: 0.7998 (mptt) REVERT: H 283 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: I 139 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.6364 (t80) REVERT: I 256 GLN cc_start: 0.6991 (tp-100) cc_final: 0.6786 (tp40) REVERT: I 382 ASN cc_start: 0.4538 (m-40) cc_final: 0.4160 (m-40) REVERT: I 399 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.5374 (t80) REVERT: J 47 ARG cc_start: 0.8472 (ttm110) cc_final: 0.8174 (ttm110) REVERT: J 57 ASP cc_start: 0.6049 (t0) cc_final: 0.5815 (t0) REVERT: K 82 GLN cc_start: 0.7293 (tm-30) cc_final: 0.6861 (mt0) REVERT: K 95 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7686 (mp10) outliers start: 93 outliers final: 60 residues processed: 275 average time/residue: 0.3801 time to fit residues: 168.4126 Evaluate side-chains 265 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 190 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 284 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain I residue 462 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 10.0000 chunk 259 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 169 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27069 Z= 0.301 Angle : 0.597 15.854 36950 Z= 0.309 Chirality : 0.042 0.243 3957 Planarity : 0.004 0.088 4421 Dihedral : 16.303 175.422 4514 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.81 % Favored : 93.92 % Rotamer: Outliers : 3.78 % Allowed : 19.58 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.07 (0.16), residues: 2943 helix: 1.20 (0.16), residues: 1028 sheet: -0.78 (0.23), residues: 545 loop : -0.40 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 176 HIS 0.011 0.001 HIS A 84 PHE 0.019 0.002 PHE A 82 TYR 0.028 0.002 TYR K 54 ARG 0.009 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 196 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.5258 (OUTLIER) cc_final: 0.4975 (t0) REVERT: B 43 HIS cc_start: 0.7716 (t70) cc_final: 0.7424 (t-90) REVERT: B 77 HIS cc_start: 0.7652 (p90) cc_final: 0.6941 (p-80) REVERT: C 144 MET cc_start: 0.8425 (mtp) cc_final: 0.8223 (mtp) REVERT: C 205 MET cc_start: 0.8350 (mmm) cc_final: 0.7944 (mmm) REVERT: C 221 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: C 261 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: D 142 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7859 (ttp) REVERT: D 157 LEU cc_start: 0.8024 (mm) cc_final: 0.7580 (mp) REVERT: E 20 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8253 (p) REVERT: E 137 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7455 (tmm) REVERT: E 181 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8433 (pt0) REVERT: E 305 MET cc_start: 0.8233 (ttp) cc_final: 0.7831 (ttt) REVERT: F 42 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: F 64 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7449 (mt) REVERT: H 14 TYR cc_start: 0.7690 (m-80) cc_final: 0.7378 (m-80) REVERT: H 77 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7994 (tmm-80) REVERT: H 113 GLU cc_start: 0.7693 (pp20) cc_final: 0.7340 (pp20) REVERT: H 248 LYS cc_start: 0.8348 (mptt) cc_final: 0.7909 (mptt) REVERT: H 283 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7602 (mt0) REVERT: I 139 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.6476 (t80) REVERT: I 256 GLN cc_start: 0.7253 (tp-100) cc_final: 0.6974 (tp40) REVERT: I 382 ASN cc_start: 0.4572 (m-40) cc_final: 0.4214 (m110) REVERT: I 389 MET cc_start: 0.3553 (tpt) cc_final: 0.3245 (tpt) REVERT: J 47 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8098 (ttm110) REVERT: J 95 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: K 71 ARG cc_start: 0.8574 (mtp85) cc_final: 0.7978 (mtm-85) REVERT: K 82 GLN cc_start: 0.7240 (tm-30) cc_final: 0.6974 (mt0) REVERT: K 95 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: K 98 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8523 (ttp80) REVERT: L 7 GLU cc_start: 0.8272 (tp30) cc_final: 0.8060 (tp30) outliers start: 100 outliers final: 63 residues processed: 278 average time/residue: 0.3779 time to fit residues: 168.0597 Evaluate side-chains 254 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 177 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 351 ASN Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 10.0000 chunk 32 optimal weight: 40.0000 chunk 164 optimal weight: 0.0870 chunk 210 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 287 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN H 30 ASN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.6682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27069 Z= 0.224 Angle : 0.564 15.005 36950 Z= 0.292 Chirality : 0.040 0.223 3957 Planarity : 0.004 0.092 4421 Dihedral : 16.209 175.607 4510 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.37 % Favored : 94.39 % Rotamer: Outliers : 3.25 % Allowed : 20.15 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.18 (0.16), residues: 2943 helix: 1.32 (0.16), residues: 1028 sheet: -0.71 (0.22), residues: 553 loop : -0.35 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP I 488 HIS 0.004 0.001 HIS A 84 PHE 0.020 0.001 PHE B 208 TYR 0.022 0.001 TYR K 54 ARG 0.006 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 191 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.5379 (OUTLIER) cc_final: 0.5068 (t0) REVERT: B 43 HIS cc_start: 0.7687 (t70) cc_final: 0.7428 (t-90) REVERT: B 77 HIS cc_start: 0.7631 (p90) cc_final: 0.6887 (p-80) REVERT: B 102 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.5768 (t0) REVERT: C 144 MET cc_start: 0.8418 (mtp) cc_final: 0.8216 (mtp) REVERT: C 200 MET cc_start: 0.6836 (mmp) cc_final: 0.6302 (mtt) REVERT: C 221 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: C 261 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: D 142 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7924 (ttp) REVERT: D 157 LEU cc_start: 0.7961 (mm) cc_final: 0.7576 (mp) REVERT: E 20 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8205 (p) REVERT: E 137 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7450 (tmm) REVERT: E 181 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: E 305 MET cc_start: 0.8236 (ttp) cc_final: 0.7935 (ttt) REVERT: F 42 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6575 (tt0) REVERT: F 64 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7343 (mt) REVERT: F 83 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7930 (mp0) REVERT: G 205 MET cc_start: 0.8584 (mmm) cc_final: 0.8321 (mmm) REVERT: H 14 TYR cc_start: 0.7650 (m-80) cc_final: 0.7341 (m-80) REVERT: H 77 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8034 (tmm-80) REVERT: H 113 GLU cc_start: 0.7658 (pp20) cc_final: 0.7279 (pp20) REVERT: H 179 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.6629 (mtp85) REVERT: H 248 LYS cc_start: 0.8382 (mptt) cc_final: 0.8022 (mptt) REVERT: H 283 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: I 139 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6476 (t80) REVERT: I 256 GLN cc_start: 0.7211 (tp-100) cc_final: 0.6945 (tp40) REVERT: I 382 ASN cc_start: 0.4578 (m-40) cc_final: 0.4242 (m110) REVERT: I 389 MET cc_start: 0.3726 (tpt) cc_final: 0.3364 (tpt) REVERT: I 399 TYR cc_start: 0.6593 (OUTLIER) cc_final: 0.5586 (t80) REVERT: J 47 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8056 (ttm110) REVERT: J 95 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: K 71 ARG cc_start: 0.8556 (mtp85) cc_final: 0.7946 (mtm-85) REVERT: K 82 GLN cc_start: 0.7249 (tm-30) cc_final: 0.7003 (mt0) REVERT: K 95 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: K 98 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8404 (ttp80) REVERT: L 7 GLU cc_start: 0.8273 (tp30) cc_final: 0.8043 (tp30) outliers start: 86 outliers final: 57 residues processed: 263 average time/residue: 0.3957 time to fit residues: 165.8892 Evaluate side-chains 250 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 176 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 0.2980 chunk 86 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 40.0000 chunk 182 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN F 181 GLN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27069 Z= 0.160 Angle : 0.528 12.272 36950 Z= 0.275 Chirality : 0.039 0.207 3957 Planarity : 0.004 0.094 4421 Dihedral : 16.108 178.274 4510 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.27 % Favored : 94.53 % Rotamer: Outliers : 2.80 % Allowed : 20.76 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.35 (0.16), residues: 2943 helix: 1.46 (0.16), residues: 1028 sheet: -0.64 (0.22), residues: 560 loop : -0.24 (0.18), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP I 488 HIS 0.003 0.001 HIS I 183 PHE 0.021 0.001 PHE B 208 TYR 0.023 0.001 TYR L 54 ARG 0.006 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 192 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.5433 (OUTLIER) cc_final: 0.5083 (t0) REVERT: A 207 MET cc_start: 0.7591 (ttt) cc_final: 0.7239 (ttt) REVERT: B 43 HIS cc_start: 0.7661 (t70) cc_final: 0.7425 (t-90) REVERT: B 77 HIS cc_start: 0.7599 (p90) cc_final: 0.6817 (p-80) REVERT: B 141 ASN cc_start: 0.6731 (m110) cc_final: 0.6340 (t0) REVERT: C 144 MET cc_start: 0.8301 (mtp) cc_final: 0.8084 (mtp) REVERT: C 200 MET cc_start: 0.6811 (mmp) cc_final: 0.6235 (mtt) REVERT: C 221 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: C 261 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7849 (mm-30) REVERT: D 142 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8029 (ttp) REVERT: D 157 LEU cc_start: 0.7850 (mm) cc_final: 0.7471 (mp) REVERT: E 20 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8071 (p) REVERT: E 137 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7555 (tmm) REVERT: E 305 MET cc_start: 0.8226 (ttp) cc_final: 0.7932 (ttt) REVERT: F 64 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7182 (mt) REVERT: G 205 MET cc_start: 0.8583 (mmm) cc_final: 0.8302 (mmm) REVERT: H 14 TYR cc_start: 0.7589 (m-80) cc_final: 0.7313 (m-80) REVERT: H 77 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8001 (tmm-80) REVERT: H 113 GLU cc_start: 0.7648 (pp20) cc_final: 0.7321 (pp20) REVERT: H 179 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.6719 (mtp85) REVERT: H 248 LYS cc_start: 0.8354 (mptt) cc_final: 0.8066 (mptt) REVERT: H 283 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: I 20 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6960 (pt) REVERT: I 139 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.6475 (t80) REVERT: I 202 LEU cc_start: 0.6072 (mt) cc_final: 0.5847 (mt) REVERT: I 256 GLN cc_start: 0.7158 (tp-100) cc_final: 0.6918 (tp40) REVERT: I 382 ASN cc_start: 0.4282 (m-40) cc_final: 0.3884 (m-40) REVERT: I 399 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.5678 (t80) REVERT: I 442 TYR cc_start: 0.6345 (t80) cc_final: 0.5861 (t80) REVERT: J 47 ARG cc_start: 0.8432 (ttm110) cc_final: 0.8039 (ttm110) REVERT: K 22 MET cc_start: 0.8433 (ptm) cc_final: 0.7966 (ptm) REVERT: K 71 ARG cc_start: 0.8556 (mtp85) cc_final: 0.7982 (mtm-85) REVERT: K 82 GLN cc_start: 0.7256 (tm-30) cc_final: 0.7017 (tm-30) REVERT: K 95 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: K 98 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8460 (ttp80) REVERT: L 7 GLU cc_start: 0.8266 (tp30) cc_final: 0.8051 (tp30) REVERT: L 30 TYR cc_start: 0.4041 (OUTLIER) cc_final: 0.3634 (m-80) outliers start: 74 outliers final: 44 residues processed: 253 average time/residue: 0.3979 time to fit residues: 160.5399 Evaluate side-chains 242 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 183 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 362 PHE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 30 TYR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 253 optimal weight: 20.0000 chunk 266 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 ASN ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN F 181 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 294 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 27069 Z= 0.443 Angle : 0.659 17.705 36950 Z= 0.341 Chirality : 0.044 0.277 3957 Planarity : 0.005 0.096 4421 Dihedral : 16.258 175.757 4508 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.01 % Favored : 93.68 % Rotamer: Outliers : 3.44 % Allowed : 20.34 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.07 (0.16), residues: 2943 helix: 1.16 (0.16), residues: 1028 sheet: -0.53 (0.22), residues: 561 loop : -0.48 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP I 488 HIS 0.008 0.001 HIS E 31 PHE 0.026 0.002 PHE L 61 TYR 0.025 0.002 TYR K 54 ARG 0.007 0.001 ARG I 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 181 time to evaluate : 3.276 Fit side-chains revert: symmetry clash REVERT: A 196 ASP cc_start: 0.5646 (OUTLIER) cc_final: 0.5195 (t0) REVERT: B 43 HIS cc_start: 0.7621 (t70) cc_final: 0.7379 (t-90) REVERT: B 77 HIS cc_start: 0.7551 (p90) cc_final: 0.6812 (p90) REVERT: B 102 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.5840 (t70) REVERT: C 200 MET cc_start: 0.6792 (mmp) cc_final: 0.6342 (mtt) REVERT: C 221 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: C 261 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8069 (mm-30) REVERT: E 137 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7431 (tmm) REVERT: E 284 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8349 (mt0) REVERT: E 305 MET cc_start: 0.8238 (ttp) cc_final: 0.7840 (ttt) REVERT: F 42 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6758 (tt0) REVERT: F 64 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7531 (mt) REVERT: G 205 MET cc_start: 0.8657 (mmm) cc_final: 0.8353 (mmm) REVERT: H 14 TYR cc_start: 0.7738 (m-80) cc_final: 0.7456 (m-80) REVERT: H 77 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8166 (tmm-80) REVERT: H 113 GLU cc_start: 0.7601 (pp20) cc_final: 0.7261 (pp20) REVERT: H 179 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7312 (mtp85) REVERT: H 248 LYS cc_start: 0.8425 (mptt) cc_final: 0.7946 (mptt) REVERT: H 283 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: I 139 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6582 (t80) REVERT: I 202 LEU cc_start: 0.6250 (mt) cc_final: 0.6040 (mt) REVERT: I 382 ASN cc_start: 0.4732 (m-40) cc_final: 0.4426 (m110) REVERT: I 399 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.5493 (t80) REVERT: J 47 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8024 (ttm110) REVERT: J 95 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: K 71 ARG cc_start: 0.8543 (mtp85) cc_final: 0.7881 (mtm-85) REVERT: K 82 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6924 (mt0) REVERT: K 95 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7753 (mp10) REVERT: L 30 TYR cc_start: 0.4108 (OUTLIER) cc_final: 0.3678 (m-80) outliers start: 91 outliers final: 56 residues processed: 256 average time/residue: 0.3974 time to fit residues: 161.6364 Evaluate side-chains 248 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 177 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 362 PHE Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 30 TYR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 0.7980 chunk 283 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 296 optimal weight: 10.0000 chunk 273 optimal weight: 30.0000 chunk 236 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN F 256 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 GLN I 256 GLN I 294 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27069 Z= 0.224 Angle : 0.577 14.509 36950 Z= 0.298 Chirality : 0.041 0.228 3957 Planarity : 0.004 0.098 4421 Dihedral : 16.144 176.086 4508 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.33 % Favored : 94.39 % Rotamer: Outliers : 2.42 % Allowed : 21.32 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.24 (0.16), residues: 2943 helix: 1.33 (0.16), residues: 1025 sheet: -0.52 (0.23), residues: 532 loop : -0.36 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP I 488 HIS 0.004 0.001 HIS E 31 PHE 0.022 0.001 PHE B 208 TYR 0.021 0.001 TYR F 244 ARG 0.007 0.000 ARG I 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 182 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.5792 (OUTLIER) cc_final: 0.5255 (t0) REVERT: B 43 HIS cc_start: 0.7652 (t70) cc_final: 0.7425 (t-90) REVERT: B 77 HIS cc_start: 0.7578 (p90) cc_final: 0.6816 (p90) REVERT: B 102 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.5770 (t0) REVERT: C 35 ARG cc_start: 0.7627 (mmm160) cc_final: 0.7167 (tpm170) REVERT: C 200 MET cc_start: 0.6828 (mmp) cc_final: 0.6145 (mtt) REVERT: C 221 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: C 261 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: D 157 LEU cc_start: 0.7927 (mm) cc_final: 0.7540 (mp) REVERT: E 137 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7437 (tmm) REVERT: E 284 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8441 (mt0) REVERT: E 305 MET cc_start: 0.8217 (ttp) cc_final: 0.7792 (ttt) REVERT: F 64 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7368 (mt) REVERT: G 205 MET cc_start: 0.8616 (mmm) cc_final: 0.8376 (mmm) REVERT: H 14 TYR cc_start: 0.7585 (m-80) cc_final: 0.7316 (m-80) REVERT: H 77 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8014 (tmm-80) REVERT: H 113 GLU cc_start: 0.7599 (pp20) cc_final: 0.7248 (pp20) REVERT: H 179 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.6686 (mtp85) REVERT: H 248 LYS cc_start: 0.8409 (mptt) cc_final: 0.8003 (mptt) REVERT: H 283 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: I 139 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6576 (t80) REVERT: I 202 LEU cc_start: 0.5953 (mt) cc_final: 0.5747 (mt) REVERT: I 382 ASN cc_start: 0.4502 (m-40) cc_final: 0.4180 (m110) REVERT: I 399 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.5482 (t80) REVERT: J 47 ARG cc_start: 0.8430 (ttm110) cc_final: 0.8012 (ttm110) REVERT: J 95 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: K 60 SER cc_start: 0.9046 (t) cc_final: 0.8808 (p) REVERT: K 71 ARG cc_start: 0.8536 (mtp85) cc_final: 0.7949 (mtm-85) REVERT: K 82 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6893 (tm-30) REVERT: K 95 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7910 (mp10) REVERT: L 6 GLU cc_start: 0.7915 (tp30) cc_final: 0.7673 (tp30) REVERT: L 30 TYR cc_start: 0.4106 (OUTLIER) cc_final: 0.3668 (m-80) outliers start: 64 outliers final: 43 residues processed: 236 average time/residue: 0.3944 time to fit residues: 148.5419 Evaluate side-chains 237 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 180 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 362 PHE Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 30 TYR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 0.9980 chunk 251 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 217 optimal weight: 9.9990 chunk 34 optimal weight: 40.0000 chunk 65 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN J 4 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.134077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.099696 restraints weight = 56859.293| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.13 r_work: 0.3431 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27069 Z= 0.307 Angle : 0.608 15.483 36950 Z= 0.313 Chirality : 0.041 0.252 3957 Planarity : 0.004 0.101 4421 Dihedral : 16.176 176.262 4508 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.12 % Favored : 93.61 % Rotamer: Outliers : 2.65 % Allowed : 21.17 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.18 (0.16), residues: 2943 helix: 1.27 (0.16), residues: 1028 sheet: -0.52 (0.23), residues: 532 loop : -0.40 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP I 488 HIS 0.004 0.001 HIS I 149 PHE 0.048 0.002 PHE I 152 TYR 0.021 0.002 TYR K 54 ARG 0.007 0.000 ARG I 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5406.42 seconds wall clock time: 99 minutes 55.29 seconds (5995.29 seconds total)