Starting phenix.real_space_refine on Tue Feb 20 13:25:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff5_29040/02_2024/8ff5_29040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff5_29040/02_2024/8ff5_29040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff5_29040/02_2024/8ff5_29040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff5_29040/02_2024/8ff5_29040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff5_29040/02_2024/8ff5_29040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff5_29040/02_2024/8ff5_29040.pdb" } resolution = 3.13 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= 0.005 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 859 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 136 5.49 5 S 94 5.16 5 C 16944 2.51 5 N 4614 2.21 5 O 5336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "H TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 251": "OE1" <-> "OE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 194": "OE1" <-> "OE2" Residue "I GLU 235": "OE1" <-> "OE2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "I GLU 446": "OE1" <-> "OE2" Residue "I GLU 468": "OE1" <-> "OE2" Residue "I GLU 471": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L GLU 35": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" 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: 27124 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: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1702 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2330 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "H" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 26, 'rna3p': 36} Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1079 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "O" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Time building chain proxies: 14.72, per 1000 atoms: 0.54 Number of scatterers: 27124 At special positions: 0 Unit cell: (110.67, 129.642, 219.232, 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 136 15.00 O 5336 8.00 N 4614 7.00 C 16944 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: 12.21 Conformation dependent library (CDL) restraints added in 4.2 seconds 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5546 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 44 sheets defined 39.3% alpha, 21.2% beta 47 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 8.84 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 40 through 44 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 142 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.635A 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: 3.617A 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 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' 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: 3.873A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.898A 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 285 removed outlier: 3.611A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.535A pdb=" N MET C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) 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 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: 3.645A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.752A 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: 4.018A 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 removed outlier: 3.612A pdb=" N MET D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.586A 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: 3.772A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 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 285 removed outlier: 3.911A 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 removed outlier: 3.645A pdb=" N MET E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.634A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.933A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.532A 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: 3.716A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 removed outlier: 3.542A pdb=" N MET F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) 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 72 removed outlier: 3.749A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 104 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: 3.671A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.518A pdb=" N ILE G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) 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: 3.950A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 296 Processing helix chain 'G' and resid 301 through 317 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: 3.526A 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 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: 3.672A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.886A 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 284 removed outlier: 3.946A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 Processing helix chain 'H' and resid 301 through 318 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 42 through 50 removed outlier: 5.246A pdb=" N GLY I 47 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY I 48 " --> pdb=" O GLN I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.940A 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 152 through 157 Processing helix chain 'I' and resid 183 through 187 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 253 through 257 removed outlier: 3.572A pdb=" N PHE I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 253 through 257' Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 removed outlier: 3.642A pdb=" N SER I 346 " --> pdb=" O ASN I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 367 Processing helix chain 'I' and resid 373 through 393 removed outlier: 3.956A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY I 385 " --> pdb=" O SER I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 421 removed outlier: 4.545A pdb=" N TYR I 399 " --> pdb=" O GLU I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 Processing helix chain 'I' and resid 445 through 461 removed outlier: 3.755A pdb=" N GLY I 461 " --> pdb=" O LEU I 457 " (cutoff:3.500A) 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 5 through 33 Processing helix chain 'J' and resid 41 through 54 Processing helix chain 'J' and resid 58 through 73 removed outlier: 6.086A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 Processing helix chain 'J' and resid 93 through 108 Processing helix chain 'J' and resid 109 through 112 Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 Processing helix chain 'K' and resid 58 through 73 removed outlier: 6.029A pdb=" N TYR K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 81 removed outlier: 3.769A pdb=" N HIS K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 91 removed outlier: 4.059A pdb=" N ILE K 85 " --> pdb=" O HIS K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 109 removed outlier: 4.606A pdb=" N LYS K 109 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.800A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 removed outlier: 3.550A pdb=" N HIS L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 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: 3.984A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.568A pdb=" N LEU A 57 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ARG A 165 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 160 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 6.915A 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: 6.994A pdb=" N ILE A 6 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TRP A 104 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 8 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 102 " --> pdb=" O TYR A 8 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP A 10 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 100 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.489A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.489A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (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: 6.294A pdb=" N PHE B 177 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 119 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.555A 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: 5.555A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.665A 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 Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB4, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 225 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 276 " --> pdb=" O TYR D 299 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 156 Processing sheet with id=AB9, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.620A pdb=" N SER E 225 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 276 " --> pdb=" O TYR E 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.565A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'E' and resid 155 through 159 Processing sheet with id=AC7, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR F 182 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR F 15 " --> pdb=" O TRP F 230 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TRP F 230 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR F 17 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE F 228 " --> pdb=" O TYR F 17 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR F 19 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU F 226 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU F 21 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 276 " --> pdb=" O TYR F 299 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.690A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD3, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.398A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR G 183 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA G 145 " --> pdb=" O GLN G 181 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLN G 181 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 225 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.782A pdb=" N GLY G 25 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'G' and resid 77 through 80 Processing sheet with id=AD7, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD8, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.422A 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: 6.904A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE2, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE3, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.081A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 61 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 11 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AE5, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.592A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AE7, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.376A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 332 through 333 1087 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 10.13 Time building geometry restraints manager: 13.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8138 1.34 - 1.46: 7686 1.46 - 1.59: 11827 1.59 - 1.71: 266 1.71 - 1.84: 149 Bond restraints: 28066 Sorted by residual: bond pdb=" CA ASP D 246 " pdb=" C ASP D 246 " ideal model delta sigma weight residual 1.524 1.508 0.016 8.10e-03 1.52e+04 3.84e+00 bond pdb=" O3' DC N 50 " pdb=" P DT N 51 " ideal model delta sigma weight residual 1.607 1.635 -0.028 1.50e-02 4.44e+03 3.51e+00 bond pdb=" C PRO A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 1.329 1.350 -0.020 1.25e-02 6.40e+03 2.60e+00 bond pdb=" CA VAL I 205 " pdb=" C VAL I 205 " ideal model delta sigma weight residual 1.520 1.534 -0.014 8.80e-03 1.29e+04 2.49e+00 bond pdb=" C LEU I 379 " pdb=" O LEU I 379 " ideal model delta sigma weight residual 1.236 1.219 0.018 1.15e-02 7.56e+03 2.45e+00 ... (remaining 28061 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.42: 814 104.42 - 111.83: 13284 111.83 - 119.24: 9466 119.24 - 126.66: 14205 126.66 - 134.07: 745 Bond angle restraints: 38514 Sorted by residual: angle pdb=" C THR B 157 " pdb=" N PRO B 158 " pdb=" CA PRO B 158 " ideal model delta sigma weight residual 119.76 115.31 4.45 1.03e+00 9.43e-01 1.87e+01 angle pdb=" N GLY I 355 " pdb=" CA GLY I 355 " pdb=" C GLY I 355 " ideal model delta sigma weight residual 115.21 109.83 5.38 1.30e+00 5.92e-01 1.71e+01 angle pdb=" C ILE B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 120.49 126.34 -5.85 1.42e+00 4.96e-01 1.70e+01 angle pdb=" C PRO A 200 " pdb=" N PRO A 201 " pdb=" CA PRO A 201 " ideal model delta sigma weight residual 120.14 115.79 4.35 1.06e+00 8.90e-01 1.68e+01 angle pdb=" N GLN I 45 " pdb=" CA GLN I 45 " pdb=" C GLN I 45 " ideal model delta sigma weight residual 112.23 107.18 5.05 1.26e+00 6.30e-01 1.61e+01 ... (remaining 38509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 15733 35.81 - 71.62: 822 71.62 - 107.43: 60 107.43 - 143.24: 4 143.24 - 179.04: 5 Dihedral angle restraints: 16624 sinusoidal: 7965 harmonic: 8659 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 20.96 179.04 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 60.29 139.71 1 1.50e+01 4.44e-03 7.52e+01 dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual 232.00 66.54 165.46 1 1.70e+01 3.46e-03 6.54e+01 ... (remaining 16621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3317 0.046 - 0.091: 623 0.091 - 0.137: 174 0.137 - 0.183: 14 0.183 - 0.228: 5 Chirality restraints: 4133 Sorted by residual: chirality pdb=" C3' A M 38 " pdb=" C4' A M 38 " pdb=" O3' A M 38 " pdb=" C2' A M 38 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE J 13 " pdb=" CA ILE J 13 " pdb=" CG1 ILE J 13 " pdb=" CG2 ILE J 13 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA MET A 1 " pdb=" N MET A 1 " pdb=" C MET A 1 " pdb=" CB MET A 1 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4130 not shown) Planarity restraints: 4439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " 0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO F 247 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C PHE J 61 " 0.056 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 246 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO E 247 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 247 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 247 " 0.041 5.00e-02 4.00e+02 ... (remaining 4436 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 190 2.49 - 3.09: 19801 3.09 - 3.69: 44453 3.69 - 4.30: 65577 4.30 - 4.90: 104498 Nonbonded interactions: 234519 Sorted by model distance: nonbonded pdb=" C5' DG O 10 " pdb=" O6 DG O 11 " model vdw 1.886 3.440 nonbonded pdb=" O4 U M 35 " pdb=" N6 A M 36 " model vdw 2.163 2.520 nonbonded pdb=" O4 U M 23 " pdb=" N6 A M 24 " model vdw 2.164 2.520 nonbonded pdb=" C5' DG O 10 " pdb=" C6 DG O 11 " model vdw 2.185 3.660 nonbonded pdb=" OG SER E 28 " pdb=" O GLU E 174 " model vdw 2.211 2.440 ... (remaining 234514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 5.100 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 77.430 Find NCS groups from input model: 1.290 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 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 0.060 28066 Z= 0.206 Angle : 0.657 10.079 38514 Z= 0.377 Chirality : 0.040 0.228 4133 Planarity : 0.005 0.088 4439 Dihedral : 19.538 179.045 11078 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.16 % Favored : 92.16 % Rotamer: Outliers : 0.95 % Allowed : 20.05 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.20 (0.16), residues: 2921 helix: 1.34 (0.16), residues: 1001 sheet: -0.86 (0.20), residues: 619 loop : -0.87 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP I 63 HIS 0.005 0.001 HIS H 171 PHE 0.019 0.001 PHE G 234 TYR 0.038 0.001 TYR C 244 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 368 time to evaluate : 3.061 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: 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 167 ASN cc_start: 0.8214 (m-40) cc_final: 0.7879 (p0) REVERT: C 155 VAL cc_start: 0.8718 (p) cc_final: 0.8509 (p) REVERT: C 172 PHE cc_start: 0.6419 (m-10) cc_final: 0.5925 (m-10) REVERT: E 15 TYR cc_start: 0.8489 (m-80) cc_final: 0.8186 (m-80) REVERT: E 108 LEU cc_start: 0.8204 (tt) cc_final: 0.7872 (tt) REVERT: E 248 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7475 (mptt) REVERT: F 48 ASN cc_start: 0.8678 (m-40) cc_final: 0.8408 (t0) REVERT: F 144 MET cc_start: 0.8830 (mtm) cc_final: 0.8242 (mtm) REVERT: F 205 MET cc_start: 0.8489 (mmp) cc_final: 0.8078 (mmm) REVERT: G 135 GLN cc_start: 0.8447 (pt0) cc_final: 0.8182 (pt0) REVERT: I 310 ILE cc_start: 0.7768 (mt) cc_final: 0.6967 (mm) REVERT: I 443 CYS cc_start: 0.8878 (m) cc_final: 0.8653 (m) REVERT: J 38 ASP cc_start: 0.6373 (t0) cc_final: 0.6117 (m-30) REVERT: J 53 ASN cc_start: 0.7992 (t0) cc_final: 0.7588 (m-40) REVERT: K 38 ASP cc_start: 0.8389 (t0) cc_final: 0.8141 (t0) REVERT: K 47 ARG cc_start: 0.8730 (ttt90) cc_final: 0.8433 (ttt90) REVERT: L 43 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8659 (tppt) REVERT: L 51 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7974 (mm-30) REVERT: L 80 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8273 (mt-10) REVERT: L 96 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8363 (mp0) outliers start: 25 outliers final: 3 residues processed: 387 average time/residue: 0.4464 time to fit residues: 261.5882 Evaluate side-chains 218 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain I residue 358 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 195 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 ASN ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 28066 Z= 0.288 Angle : 0.635 7.600 38514 Z= 0.340 Chirality : 0.041 0.255 4133 Planarity : 0.005 0.091 4439 Dihedral : 19.300 176.060 5061 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.85 % Favored : 92.57 % Rotamer: Outliers : 3.66 % Allowed : 18.75 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.11 (0.16), residues: 2921 helix: 1.61 (0.16), residues: 1007 sheet: -0.65 (0.22), residues: 558 loop : -0.75 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 73 HIS 0.006 0.001 HIS J 81 PHE 0.022 0.002 PHE G 234 TYR 0.026 0.002 TYR A 175 ARG 0.008 0.001 ARG L 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 213 time to evaluate : 2.833 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: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7173 (t0) cc_final: 0.6855 (t0) REVERT: A 167 ASN cc_start: 0.8294 (m-40) cc_final: 0.8075 (p0) REVERT: B 98 PHE cc_start: 0.4186 (OUTLIER) cc_final: 0.3508 (t80) REVERT: B 116 TYR cc_start: 0.4285 (OUTLIER) cc_final: 0.3900 (t80) REVERT: E 137 MET cc_start: 0.8456 (tpt) cc_final: 0.8132 (tpt) REVERT: E 248 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7910 (mptt) REVERT: F 48 ASN cc_start: 0.8719 (m-40) cc_final: 0.8432 (t0) REVERT: F 108 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8532 (tt) REVERT: F 142 MET cc_start: 0.9178 (tpp) cc_final: 0.8977 (mmm) REVERT: F 144 MET cc_start: 0.8914 (mtm) cc_final: 0.8501 (mtm) REVERT: F 205 MET cc_start: 0.8682 (mmp) cc_final: 0.8316 (mmm) REVERT: F 219 TYR cc_start: 0.7981 (t80) cc_final: 0.7740 (t80) REVERT: G 32 ASP cc_start: 0.7924 (p0) cc_final: 0.7632 (p0) REVERT: G 77 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8563 (ttp-170) REVERT: G 160 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8302 (mttp) REVERT: G 170 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6936 (pt) REVERT: G 221 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7839 (t80) REVERT: H 205 MET cc_start: 0.8929 (mmm) cc_final: 0.8651 (mmp) REVERT: I 74 LEU cc_start: 0.9318 (tp) cc_final: 0.9044 (pp) REVERT: I 187 GLN cc_start: 0.8486 (pm20) cc_final: 0.8170 (pp30) REVERT: I 323 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7820 (mmtt) REVERT: I 443 CYS cc_start: 0.8773 (m) cc_final: 0.8458 (m) REVERT: J 38 ASP cc_start: 0.6590 (t0) cc_final: 0.6276 (m-30) REVERT: K 38 ASP cc_start: 0.8527 (t0) cc_final: 0.8244 (t0) REVERT: L 51 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8025 (mm-30) REVERT: L 97 ILE cc_start: 0.9332 (mm) cc_final: 0.8980 (mt) outliers start: 96 outliers final: 29 residues processed: 298 average time/residue: 0.4040 time to fit residues: 188.3159 Evaluate side-chains 221 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 281 ASP 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 142 MET Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 112 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 228 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 274 optimal weight: 0.8980 chunk 296 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 30 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS E 266 GLN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 HIS I 88 HIS ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 28066 Z= 0.405 Angle : 0.676 11.676 38514 Z= 0.360 Chirality : 0.043 0.203 4133 Planarity : 0.005 0.092 4439 Dihedral : 19.301 172.662 5057 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.09 % Favored : 92.30 % Rotamer: Outliers : 3.47 % Allowed : 18.71 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2921 helix: 1.34 (0.16), residues: 1009 sheet: -0.70 (0.22), residues: 558 loop : -0.75 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 104 HIS 0.006 0.001 HIS G 31 PHE 0.020 0.002 PHE L 26 TYR 0.025 0.002 TYR F 244 ARG 0.012 0.001 ARG I 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 193 time to evaluate : 2.923 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 24 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7607 (tpp) REVERT: A 113 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8970 (mm-40) REVERT: A 166 ASP cc_start: 0.7518 (t0) cc_final: 0.7218 (t0) REVERT: A 167 ASN cc_start: 0.8340 (m-40) cc_final: 0.8031 (p0) REVERT: B 98 PHE cc_start: 0.4026 (OUTLIER) cc_final: 0.3506 (t80) REVERT: B 116 TYR cc_start: 0.4370 (OUTLIER) cc_final: 0.3877 (t80) REVERT: C 295 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8551 (tptp) REVERT: D 135 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6825 (mp10) REVERT: D 137 MET cc_start: 0.8340 (tpp) cc_final: 0.8042 (tpp) REVERT: E 244 TYR cc_start: 0.5129 (p90) cc_final: 0.4860 (p90) REVERT: E 248 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8358 (mptt) REVERT: F 144 MET cc_start: 0.9005 (mtm) cc_final: 0.8799 (mtm) REVERT: F 205 MET cc_start: 0.8713 (mmp) cc_final: 0.8280 (mmm) REVERT: G 77 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7640 (mtm-85) REVERT: G 137 MET cc_start: 0.8554 (tpp) cc_final: 0.8096 (tpp) REVERT: G 170 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6811 (pt) REVERT: G 226 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9072 (mp) REVERT: I 323 LYS cc_start: 0.8434 (mmmt) cc_final: 0.7964 (mmtt) REVERT: I 443 CYS cc_start: 0.8871 (m) cc_final: 0.8527 (m) REVERT: J 38 ASP cc_start: 0.6640 (t0) cc_final: 0.6250 (m-30) REVERT: K 38 ASP cc_start: 0.8611 (t0) cc_final: 0.8319 (t0) REVERT: K 47 ARG cc_start: 0.8482 (ttt90) cc_final: 0.8276 (ttt90) REVERT: L 51 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7982 (mm-30) outliers start: 91 outliers final: 41 residues processed: 270 average time/residue: 0.4276 time to fit residues: 180.2049 Evaluate side-chains 216 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 166 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 VAL 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 77 ARG Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 235 GLU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 184 ASN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 284 GLN F 30 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN K 4 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28066 Z= 0.169 Angle : 0.574 9.425 38514 Z= 0.307 Chirality : 0.039 0.190 4133 Planarity : 0.004 0.091 4439 Dihedral : 19.169 168.843 5057 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.81 % Favored : 92.71 % Rotamer: Outliers : 2.52 % Allowed : 19.86 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 2921 helix: 1.52 (0.16), residues: 1014 sheet: -0.66 (0.22), residues: 553 loop : -0.71 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 73 HIS 0.006 0.001 HIS H 171 PHE 0.017 0.001 PHE G 234 TYR 0.018 0.001 TYR L 11 ARG 0.011 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 185 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8967 (mm-40) REVERT: A 140 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7771 (tp30) REVERT: A 166 ASP cc_start: 0.7332 (t0) cc_final: 0.7081 (t0) REVERT: A 167 ASN cc_start: 0.8221 (m-40) cc_final: 0.7933 (p0) REVERT: B 98 PHE cc_start: 0.4232 (OUTLIER) cc_final: 0.3627 (t80) REVERT: B 116 TYR cc_start: 0.4094 (OUTLIER) cc_final: 0.3849 (t80) REVERT: D 137 MET cc_start: 0.8057 (tpp) cc_final: 0.7834 (tmm) REVERT: D 305 MET cc_start: 0.8095 (tmm) cc_final: 0.7821 (tmm) REVERT: E 77 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7896 (ttp-170) REVERT: E 244 TYR cc_start: 0.5352 (p90) cc_final: 0.4936 (p90) REVERT: F 142 MET cc_start: 0.9165 (tpp) cc_final: 0.8957 (mmm) REVERT: F 144 MET cc_start: 0.8808 (mtm) cc_final: 0.8413 (mtp) REVERT: F 219 TYR cc_start: 0.8246 (t80) cc_final: 0.8022 (t80) REVERT: F 268 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8694 (p0) REVERT: F 283 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8584 (mp10) REVERT: G 77 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7760 (mtm-85) REVERT: G 170 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6805 (pt) REVERT: I 74 LEU cc_start: 0.9293 (tp) cc_final: 0.9011 (pp) REVERT: I 323 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8076 (mmtt) REVERT: I 439 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7881 (tp30) REVERT: I 443 CYS cc_start: 0.8744 (m) cc_final: 0.8317 (m) REVERT: J 38 ASP cc_start: 0.6630 (t0) cc_final: 0.6267 (m-30) REVERT: J 56 TYR cc_start: 0.8458 (p90) cc_final: 0.8038 (p90) REVERT: J 71 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7580 (mtt-85) REVERT: K 38 ASP cc_start: 0.8619 (t0) cc_final: 0.8336 (t0) REVERT: L 51 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7898 (mm-30) REVERT: L 96 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8517 (tp30) outliers start: 66 outliers final: 31 residues processed: 239 average time/residue: 0.4116 time to fit residues: 156.0489 Evaluate side-chains 213 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 217 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 262 optimal weight: 0.0040 chunk 73 optimal weight: 0.1980 overall best weight: 1.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 284 GLN F 30 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 ASN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 GLN ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28066 Z= 0.196 Angle : 0.555 7.420 38514 Z= 0.298 Chirality : 0.039 0.196 4133 Planarity : 0.004 0.092 4439 Dihedral : 19.115 169.647 5053 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.78 % Favored : 92.74 % Rotamer: Outliers : 3.09 % Allowed : 19.47 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2921 helix: 1.56 (0.16), residues: 1014 sheet: -0.74 (0.21), residues: 582 loop : -0.68 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 73 HIS 0.005 0.001 HIS H 171 PHE 0.024 0.001 PHE J 78 TYR 0.016 0.001 TYR L 11 ARG 0.011 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 179 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7215 (tpp) REVERT: A 113 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8973 (mm-40) REVERT: A 140 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7815 (tp30) REVERT: A 166 ASP cc_start: 0.7366 (t0) cc_final: 0.7103 (t0) REVERT: A 167 ASN cc_start: 0.8096 (m-40) cc_final: 0.7886 (p0) REVERT: B 98 PHE cc_start: 0.4317 (OUTLIER) cc_final: 0.3682 (t80) REVERT: D 137 MET cc_start: 0.8111 (tpp) cc_final: 0.7890 (tmm) REVERT: D 305 MET cc_start: 0.8154 (tmm) cc_final: 0.7866 (tmm) REVERT: E 134 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7876 (p0) REVERT: E 244 TYR cc_start: 0.5360 (p90) cc_final: 0.4897 (p90) REVERT: F 144 MET cc_start: 0.8811 (mtm) cc_final: 0.8534 (mtp) REVERT: F 268 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8710 (p0) REVERT: F 283 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8756 (mp10) REVERT: G 77 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7711 (mtm-85) REVERT: G 170 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6836 (pt) REVERT: I 323 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8074 (mmtt) REVERT: I 389 MET cc_start: 0.1936 (mtt) cc_final: 0.1392 (mmt) REVERT: I 439 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7867 (tp30) REVERT: I 443 CYS cc_start: 0.8736 (m) cc_final: 0.8313 (m) REVERT: J 22 MET cc_start: 0.8001 (ppp) cc_final: 0.7797 (ppp) REVERT: J 38 ASP cc_start: 0.6698 (t0) cc_final: 0.6286 (m-30) REVERT: J 56 TYR cc_start: 0.8399 (p90) cc_final: 0.8009 (p90) REVERT: J 71 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7721 (mtt-85) REVERT: J 112 ASP cc_start: 0.3771 (OUTLIER) cc_final: 0.2748 (p0) REVERT: K 38 ASP cc_start: 0.8622 (t0) cc_final: 0.8341 (t0) REVERT: L 51 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7924 (mm-30) outliers start: 81 outliers final: 41 residues processed: 250 average time/residue: 0.3990 time to fit residues: 157.8390 Evaluate side-chains 218 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 170 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 8.9990 chunk 262 optimal weight: 0.0270 chunk 57 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 242 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 overall best weight: 2.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN F 30 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN I 117 ASN J 20 GLN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28066 Z= 0.247 Angle : 0.573 7.514 38514 Z= 0.307 Chirality : 0.040 0.191 4133 Planarity : 0.004 0.093 4439 Dihedral : 19.088 170.928 5053 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.88 % Favored : 92.64 % Rotamer: Outliers : 2.71 % Allowed : 19.47 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2921 helix: 1.49 (0.16), residues: 1018 sheet: -0.69 (0.21), residues: 577 loop : -0.67 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 104 HIS 0.005 0.001 HIS E 31 PHE 0.016 0.001 PHE I 132 TYR 0.020 0.001 TYR G 182 ARG 0.013 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 178 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7520 (t0) cc_final: 0.7266 (t0) REVERT: A 167 ASN cc_start: 0.8179 (m-40) cc_final: 0.7891 (p0) REVERT: B 98 PHE cc_start: 0.4146 (OUTLIER) cc_final: 0.3544 (t80) REVERT: B 139 MET cc_start: 0.3837 (ppp) cc_final: 0.3435 (ppp) REVERT: B 204 MET cc_start: -0.0629 (mtt) cc_final: -0.1034 (mtt) REVERT: D 137 MET cc_start: 0.8069 (tpp) cc_final: 0.7837 (tmm) REVERT: D 305 MET cc_start: 0.8229 (tmm) cc_final: 0.7966 (tmm) REVERT: E 134 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7915 (p0) REVERT: E 244 TYR cc_start: 0.5364 (p90) cc_final: 0.4852 (p90) REVERT: F 77 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8457 (mtm110) REVERT: F 108 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8904 (tt) REVERT: F 144 MET cc_start: 0.8897 (mtm) cc_final: 0.8531 (mtp) REVERT: F 268 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8743 (p0) REVERT: G 77 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7644 (mtm-85) REVERT: G 170 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6866 (pt) REVERT: I 303 MET cc_start: 0.8846 (mmm) cc_final: 0.8415 (mmm) REVERT: I 323 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8126 (mmtt) REVERT: I 389 MET cc_start: 0.1912 (mtt) cc_final: 0.1485 (mmp) REVERT: I 439 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7872 (tp30) REVERT: I 443 CYS cc_start: 0.8761 (m) cc_final: 0.8357 (m) REVERT: J 22 MET cc_start: 0.7912 (ppp) cc_final: 0.7679 (ppp) REVERT: J 38 ASP cc_start: 0.6593 (t0) cc_final: 0.6208 (m-30) REVERT: J 56 TYR cc_start: 0.8399 (p90) cc_final: 0.8068 (p90) REVERT: J 71 ARG cc_start: 0.8317 (mtt180) cc_final: 0.7815 (mtt-85) REVERT: J 112 ASP cc_start: 0.3843 (OUTLIER) cc_final: 0.2796 (p0) REVERT: K 38 ASP cc_start: 0.8602 (t0) cc_final: 0.8315 (t0) REVERT: L 51 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7895 (mm-30) outliers start: 71 outliers final: 43 residues processed: 237 average time/residue: 0.4199 time to fit residues: 155.6560 Evaluate side-chains 219 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 168 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 9.9990 chunk 32 optimal weight: 50.0000 chunk 166 optimal weight: 7.9990 chunk 213 optimal weight: 30.0000 chunk 165 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 chunk 163 optimal weight: 6.9990 chunk 291 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 GLN J 82 GLN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 28066 Z= 0.454 Angle : 0.696 8.993 38514 Z= 0.370 Chirality : 0.044 0.205 4133 Planarity : 0.005 0.092 4439 Dihedral : 19.233 171.142 5053 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.63 % Favored : 91.78 % Rotamer: Outliers : 2.71 % Allowed : 20.66 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.23 (0.16), residues: 2921 helix: 1.08 (0.16), residues: 1026 sheet: -0.77 (0.22), residues: 571 loop : -0.78 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 104 HIS 0.013 0.001 HIS F 31 PHE 0.035 0.002 PHE G 234 TYR 0.023 0.002 TYR F 244 ARG 0.017 0.001 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 173 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7665 (tpp) REVERT: A 166 ASP cc_start: 0.7976 (t0) cc_final: 0.7704 (t0) REVERT: A 167 ASN cc_start: 0.8083 (m-40) cc_final: 0.7829 (p0) REVERT: B 98 PHE cc_start: 0.3618 (OUTLIER) cc_final: 0.3281 (t80) REVERT: B 139 MET cc_start: 0.3898 (ppp) cc_final: 0.3598 (ppp) REVERT: B 204 MET cc_start: -0.0438 (mtt) cc_final: -0.0811 (mtt) REVERT: D 137 MET cc_start: 0.8325 (tpp) cc_final: 0.8006 (tpp) REVERT: E 134 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7937 (p0) REVERT: E 244 TYR cc_start: 0.5146 (p90) cc_final: 0.4650 (p90) REVERT: E 284 GLN cc_start: 0.9321 (tp-100) cc_final: 0.9047 (tp-100) REVERT: F 77 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8447 (mtm110) REVERT: F 137 MET cc_start: 0.8075 (tpt) cc_final: 0.7655 (tpp) REVERT: G 77 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7531 (mtm-85) REVERT: G 170 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6786 (pt) REVERT: I 74 LEU cc_start: 0.9361 (tp) cc_final: 0.9060 (pp) REVERT: I 117 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6867 (p0) REVERT: I 389 MET cc_start: 0.2125 (mtt) cc_final: 0.1472 (mmp) REVERT: I 439 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8009 (tp30) REVERT: J 22 MET cc_start: 0.7992 (ppp) cc_final: 0.7701 (ppp) REVERT: J 53 ASN cc_start: 0.7755 (m-40) cc_final: 0.7463 (m-40) REVERT: J 71 ARG cc_start: 0.8480 (mtt180) cc_final: 0.7970 (mtt-85) REVERT: J 85 ILE cc_start: 0.5541 (OUTLIER) cc_final: 0.5333 (tp) REVERT: K 38 ASP cc_start: 0.8688 (t0) cc_final: 0.8397 (t0) REVERT: L 47 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8572 (tpt-90) outliers start: 71 outliers final: 50 residues processed: 235 average time/residue: 0.4263 time to fit residues: 158.1915 Evaluate side-chains 218 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 159 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 117 ASN Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 27 optimal weight: 40.0000 chunk 228 optimal weight: 10.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN F 42 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28066 Z= 0.176 Angle : 0.576 7.368 38514 Z= 0.308 Chirality : 0.039 0.225 4133 Planarity : 0.004 0.091 4439 Dihedral : 19.106 172.143 5053 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.40 % Favored : 93.12 % Rotamer: Outliers : 1.98 % Allowed : 21.46 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.04 (0.16), residues: 2921 helix: 1.48 (0.16), residues: 1011 sheet: -0.75 (0.21), residues: 583 loop : -0.70 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 104 HIS 0.007 0.001 HIS H 171 PHE 0.018 0.001 PHE G 234 TYR 0.020 0.001 TYR J 54 ARG 0.013 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 177 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7813 (tp30) REVERT: A 166 ASP cc_start: 0.7552 (t0) cc_final: 0.7350 (t0) REVERT: A 167 ASN cc_start: 0.7979 (m-40) cc_final: 0.7764 (p0) REVERT: B 98 PHE cc_start: 0.3823 (OUTLIER) cc_final: 0.3373 (t80) REVERT: B 204 MET cc_start: -0.0257 (mtt) cc_final: -0.0727 (mtt) REVERT: E 77 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7783 (ttp-170) REVERT: E 134 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8006 (p0) REVERT: E 244 TYR cc_start: 0.5303 (p90) cc_final: 0.4795 (p90) REVERT: F 77 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8448 (mtm110) REVERT: F 144 MET cc_start: 0.8676 (mtp) cc_final: 0.8392 (mtp) REVERT: F 268 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8802 (p0) REVERT: G 77 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7625 (mtm-85) REVERT: G 170 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6728 (pt) REVERT: I 303 MET cc_start: 0.8720 (mmm) cc_final: 0.8511 (mmm) REVERT: I 323 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8172 (mmtt) REVERT: I 324 TYR cc_start: 0.8186 (m-80) cc_final: 0.7944 (m-10) REVERT: I 389 MET cc_start: 0.2150 (mtt) cc_final: 0.1738 (mmp) REVERT: I 439 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7923 (tp30) REVERT: J 22 MET cc_start: 0.8007 (ppp) cc_final: 0.7737 (ppp) REVERT: J 56 TYR cc_start: 0.8357 (p90) cc_final: 0.8007 (p90) REVERT: J 71 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7921 (mtt-85) REVERT: J 112 ASP cc_start: 0.3922 (OUTLIER) cc_final: 0.2764 (p0) REVERT: K 38 ASP cc_start: 0.8643 (t0) cc_final: 0.8388 (t0) REVERT: L 47 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8477 (tpt-90) outliers start: 52 outliers final: 34 residues processed: 218 average time/residue: 0.4302 time to fit residues: 146.0389 Evaluate side-chains 210 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 256 optimal weight: 0.0470 chunk 270 optimal weight: 0.9980 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 136 GLN B 193 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN H 287 ASN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28066 Z= 0.232 Angle : 0.583 8.077 38514 Z= 0.310 Chirality : 0.040 0.238 4133 Planarity : 0.004 0.092 4439 Dihedral : 19.073 172.069 5053 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.19 % Favored : 92.33 % Rotamer: Outliers : 2.10 % Allowed : 21.57 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 2921 helix: 1.46 (0.16), residues: 1023 sheet: -0.71 (0.22), residues: 578 loop : -0.69 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 104 HIS 0.005 0.001 HIS H 171 PHE 0.023 0.001 PHE F 234 TYR 0.018 0.001 TYR I 30 ARG 0.012 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 169 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7644 (tp30) REVERT: A 166 ASP cc_start: 0.7636 (t0) cc_final: 0.7424 (t0) REVERT: A 167 ASN cc_start: 0.7994 (m-40) cc_final: 0.7759 (p0) REVERT: B 98 PHE cc_start: 0.3859 (OUTLIER) cc_final: 0.3398 (t80) REVERT: B 204 MET cc_start: -0.0172 (mtt) cc_final: -0.0644 (mtt) REVERT: E 134 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7937 (p0) REVERT: F 77 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8423 (mtm110) REVERT: F 268 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8823 (p0) REVERT: G 77 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7597 (mtm-85) REVERT: G 170 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6796 (pt) REVERT: I 324 TYR cc_start: 0.8070 (m-80) cc_final: 0.7861 (m-10) REVERT: I 439 GLU cc_start: 0.8658 (mm-30) cc_final: 0.7951 (tp30) REVERT: J 56 TYR cc_start: 0.8313 (p90) cc_final: 0.8016 (p90) REVERT: J 71 ARG cc_start: 0.8389 (mtt180) cc_final: 0.8023 (mtt90) REVERT: J 112 ASP cc_start: 0.3857 (OUTLIER) cc_final: 0.2826 (p0) REVERT: K 38 ASP cc_start: 0.8635 (t0) cc_final: 0.8370 (t0) REVERT: L 47 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8514 (tpt-90) outliers start: 55 outliers final: 39 residues processed: 213 average time/residue: 0.4288 time to fit residues: 142.2106 Evaluate side-chains 215 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 168 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28066 Z= 0.316 Angle : 0.626 8.378 38514 Z= 0.333 Chirality : 0.041 0.255 4133 Planarity : 0.005 0.092 4439 Dihedral : 19.088 172.336 5053 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.33 % Favored : 92.09 % Rotamer: Outliers : 2.02 % Allowed : 21.57 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2921 helix: 1.37 (0.16), residues: 1016 sheet: -0.70 (0.22), residues: 575 loop : -0.73 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 104 HIS 0.007 0.001 HIS E 31 PHE 0.018 0.001 PHE G 234 TYR 0.021 0.002 TYR J 54 ARG 0.013 0.000 ARG K 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 166 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7527 (tpp) REVERT: A 140 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7824 (tp30) REVERT: A 166 ASP cc_start: 0.7796 (t0) cc_final: 0.7537 (t0) REVERT: A 167 ASN cc_start: 0.7948 (m-40) cc_final: 0.7737 (p0) REVERT: B 98 PHE cc_start: 0.3875 (OUTLIER) cc_final: 0.3361 (t80) REVERT: B 139 MET cc_start: 0.3623 (ppp) cc_final: 0.2971 (ppp) REVERT: B 204 MET cc_start: -0.0312 (mtt) cc_final: -0.0717 (mtt) REVERT: C 137 MET cc_start: 0.8468 (tpt) cc_final: 0.8174 (tpt) REVERT: E 134 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7922 (p0) REVERT: F 77 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8387 (mtm110) REVERT: G 77 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7569 (mtm-85) REVERT: G 170 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6722 (pt) REVERT: I 323 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8029 (mmtt) REVERT: I 439 GLU cc_start: 0.8671 (mm-30) cc_final: 0.7989 (tp30) REVERT: J 22 MET cc_start: 0.7741 (ppp) cc_final: 0.7240 (ppp) REVERT: J 56 TYR cc_start: 0.8351 (p90) cc_final: 0.8086 (p90) REVERT: J 71 ARG cc_start: 0.8473 (mtt180) cc_final: 0.8106 (mtt90) REVERT: J 112 ASP cc_start: 0.4034 (OUTLIER) cc_final: 0.2901 (p0) REVERT: K 38 ASP cc_start: 0.8621 (t0) cc_final: 0.8300 (t0) REVERT: L 47 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8562 (tpt-90) outliers start: 53 outliers final: 40 residues processed: 210 average time/residue: 0.4169 time to fit residues: 135.5848 Evaluate side-chains 213 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 165 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 246 optimal weight: 8.9990 chunk 30 optimal weight: 40.0000 chunk 44 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.098503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.070221 restraints weight = 98186.970| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.99 r_work: 0.3246 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 28066 Z= 0.322 Angle : 0.844 59.200 38514 Z= 0.508 Chirality : 0.045 0.836 4133 Planarity : 0.006 0.131 4439 Dihedral : 19.100 172.339 5053 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.33 % Favored : 92.13 % Rotamer: Outliers : 2.06 % Allowed : 21.72 % Favored : 76.22 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2921 helix: 1.37 (0.16), residues: 1016 sheet: -0.71 (0.22), residues: 575 loop : -0.73 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 104 HIS 0.161 0.002 HIS C 233 PHE 0.017 0.001 PHE F 234 TYR 0.020 0.002 TYR I 30 ARG 0.013 0.000 ARG K 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5612.45 seconds wall clock time: 104 minutes 0.61 seconds (6240.61 seconds total)