Starting phenix.real_space_refine on Fri Mar 22 14:18:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trg_26089/03_2024/7trg_26089_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trg_26089/03_2024/7trg_26089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trg_26089/03_2024/7trg_26089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trg_26089/03_2024/7trg_26089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trg_26089/03_2024/7trg_26089_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trg_26089/03_2024/7trg_26089_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 8 5.89 5 P 16 5.49 5 Mg 8 5.21 5 S 203 5.16 5 C 21060 2.51 5 N 5865 2.21 5 O 6530 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 387": "OD1" <-> "OD2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B ASP 499": "OD1" <-> "OD2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ASP 231": "OD1" <-> "OD2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 287": "OE1" <-> "OE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 426": "OE1" <-> "OE2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E ASP 460": "OD1" <-> "OD2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "F ASP 219": "OD1" <-> "OD2" Residue "F ASP 268": "OD1" <-> "OD2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "F ASP 407": "OD1" <-> "OD2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 57": "OD1" <-> "OD2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G ASP 88": "OD1" <-> "OD2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 238": "OD1" <-> "OD2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "G ASP 358": "OD1" <-> "OD2" Residue "G GLU 440": "OE1" <-> "OE2" Residue "G GLU 479": "OE1" <-> "OE2" Residue "G ASP 529": "OD1" <-> "OD2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 341": "OD1" <-> "OD2" Residue "H ASP 342": "OD1" <-> "OD2" Residue "H ASP 521": "OD1" <-> "OD2" Residue "I ASP 59": "OD1" <-> "OD2" Residue "I GLU 66": "OE1" <-> "OE2" Residue "I ASP 86": "OD1" <-> "OD2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 491": "OE1" <-> "OE2" Residue "I ASP 519": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33714 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1316 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain breaks: 2 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "C" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4003 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 15, 'TRANS': 505} Chain breaks: 1 Chain: "D" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4063 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 18, 'TRANS': 508} Chain: "E" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3960 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 11, 'TRANS': 514} Chain: "F" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3924 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "G" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4063 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 14, 'TRANS': 520} Chain: "H" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "I" Number of atoms: 4028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4028 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 14, 'TRANS': 511} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 14.52, per 1000 atoms: 0.43 Number of scatterers: 33714 At special positions: 0 Unit cell: (180.4, 183.7, 113.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 203 16.00 P 16 15.00 Al 8 13.00 Mg 8 11.99 F 24 9.00 O 6530 8.00 N 5865 7.00 C 21060 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.16 Conformation dependent library (CDL) restraints added in 6.7 seconds 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 55 sheets defined 50.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.68 Creating SS restraints... Processing helix chain 'A' and resid 11 through 27 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 110 through 126 removed outlier: 3.742A pdb=" N SER A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.655A pdb=" N THR B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 81 through 96 Processing helix chain 'B' and resid 101 through 121 removed outlier: 4.048A pdb=" N LEU B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 146 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 157 through 169 removed outlier: 4.978A pdb=" N THR B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.798A pdb=" N ILE B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 263 through 286 removed outlier: 5.017A pdb=" N SER B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'B' and resid 320 through 328 Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 382 through 404 Processing helix chain 'B' and resid 414 through 429 removed outlier: 4.057A pdb=" N THR B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 456 removed outlier: 4.005A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 460 through 473 removed outlier: 3.932A pdb=" N GLU B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 501 through 520 Processing helix chain 'C' and resid 19 through 39 removed outlier: 4.127A pdb=" N VAL C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.821A pdb=" N ILE C 82 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.956A pdb=" N THR C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 118 through 139 Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.979A pdb=" N LEU C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 184 removed outlier: 5.085A pdb=" N ALA C 173 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 176 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 260 through 284 removed outlier: 3.868A pdb=" N GLU C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.650A pdb=" N ARG C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 326 Processing helix chain 'C' and resid 379 through 401 removed outlier: 3.559A pdb=" N ALA C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 426 removed outlier: 3.628A pdb=" N ARG C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.626A pdb=" N LEU C 442 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Proline residue: C 446 - end of helix Processing helix chain 'C' and resid 457 through 470 removed outlier: 3.554A pdb=" N GLN C 470 " --> pdb=" O ALA C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 525 Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.902A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 108 through 125 removed outlier: 3.681A pdb=" N GLU D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 150 removed outlier: 3.638A pdb=" N ASP D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 173 Processing helix chain 'D' and resid 177 through 196 removed outlier: 4.301A pdb=" N SER D 180 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS D 182 " --> pdb=" O ASN D 179 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG D 183 " --> pdb=" O SER D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 271 through 295 removed outlier: 3.759A pdb=" N LYS D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 289 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 327 through 337 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 392 through 414 Processing helix chain 'D' and resid 424 through 439 removed outlier: 3.708A pdb=" N ASP D 438 " --> pdb=" O SER D 434 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS D 439 " --> pdb=" O GLN D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 466 removed outlier: 3.772A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL D 457 " --> pdb=" O ASP D 453 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Proline residue: D 459 - end of helix Processing helix chain 'D' and resid 470 through 483 Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 510 through 529 Processing helix chain 'E' and resid 21 through 42 removed outlier: 3.503A pdb=" N VAL E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N SER E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N THR E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 79 through 94 removed outlier: 3.989A pdb=" N VAL E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 118 removed outlier: 4.196A pdb=" N THR E 103 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 143 removed outlier: 3.548A pdb=" N GLU E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 169 removed outlier: 4.811A pdb=" N SER E 169 " --> pdb=" O THR E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 190 removed outlier: 3.970A pdb=" N LYS E 176 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP E 177 " --> pdb=" O HIS E 174 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 181 " --> pdb=" O HIS E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 261 through 285 removed outlier: 3.548A pdb=" N MET E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 307 Processing helix chain 'E' and resid 317 through 327 Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 380 through 402 removed outlier: 3.812A pdb=" N ASP E 392 " --> pdb=" O ARG E 388 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 427 removed outlier: 3.894A pdb=" N ARG E 427 " --> pdb=" O GLN E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 454 removed outlier: 3.847A pdb=" N LEU E 446 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Proline residue: E 447 - end of helix Processing helix chain 'E' and resid 458 through 471 Processing helix chain 'E' and resid 488 through 491 No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 497 through 515 Processing helix chain 'F' and resid 29 through 48 Processing helix chain 'F' and resid 74 through 80 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 91 through 101 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.954A pdb=" N THR F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 151 Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'F' and resid 175 through 192 removed outlier: 4.423A pdb=" N GLN F 178 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER F 180 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER F 181 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER F 184 " --> pdb=" O SER F 181 " (cutoff:3.500A) Proline residue: F 185 - end of helix Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 269 through 293 removed outlier: 4.104A pdb=" N ASP F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 276 " --> pdb=" O MET F 272 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 286 " --> pdb=" O TYR F 282 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 319 Processing helix chain 'F' and resid 333 through 340 Processing helix chain 'F' and resid 348 through 350 No H-bonds generated for 'chain 'F' and resid 348 through 350' Processing helix chain 'F' and resid 353 through 355 No H-bonds generated for 'chain 'F' and resid 353 through 355' Processing helix chain 'F' and resid 395 through 417 Processing helix chain 'F' and resid 427 through 442 removed outlier: 3.896A pdb=" N ARG F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 469 removed outlier: 3.998A pdb=" N MET F 458 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL F 460 " --> pdb=" O ASP F 456 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) Proline residue: F 462 - end of helix Processing helix chain 'F' and resid 473 through 486 removed outlier: 3.529A pdb=" N GLN F 486 " --> pdb=" O ASN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 531 removed outlier: 3.865A pdb=" N LYS F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 32 removed outlier: 3.743A pdb=" N VAL G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 64 Processing helix chain 'G' and resid 70 through 85 removed outlier: 3.830A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 removed outlier: 3.707A pdb=" N GLU G 106 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 134 removed outlier: 3.856A pdb=" N ASN G 133 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU G 134 " --> pdb=" O ARG G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 156 Processing helix chain 'G' and resid 165 through 178 Processing helix chain 'G' and resid 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 257 through 281 removed outlier: 3.554A pdb=" N LEU G 260 " --> pdb=" O PRO G 257 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP G 261 " --> pdb=" O GLU G 258 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN G 262 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU G 267 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE G 270 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR G 271 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA G 280 " --> pdb=" O LYS G 277 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR G 281 " --> pdb=" O ILE G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 303 removed outlier: 3.843A pdb=" N LYS G 298 " --> pdb=" O ASP G 294 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR G 299 " --> pdb=" O MET G 295 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE G 300 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 323 Processing helix chain 'G' and resid 382 through 404 removed outlier: 3.732A pdb=" N ASP G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA G 395 " --> pdb=" O SER G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 426 Processing helix chain 'G' and resid 428 through 430 No H-bonds generated for 'chain 'G' and resid 428 through 430' Processing helix chain 'G' and resid 434 through 455 removed outlier: 3.936A pdb=" N LEU G 446 " --> pdb=" O ALA G 442 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL G 447 " --> pdb=" O ARG G 443 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE G 448 " --> pdb=" O SER G 444 " (cutoff:3.500A) Proline residue: G 449 - end of helix Processing helix chain 'G' and resid 460 through 475 Processing helix chain 'G' and resid 478 through 485 removed outlier: 5.468A pdb=" N ASN G 482 " --> pdb=" O GLU G 479 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 483 " --> pdb=" O ARG G 480 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP G 485 " --> pdb=" O ASN G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 501 No H-bonds generated for 'chain 'G' and resid 498 through 501' Processing helix chain 'G' and resid 507 through 525 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.042A pdb=" N ILE H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 69 removed outlier: 4.000A pdb=" N GLU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 110 through 113 No H-bonds generated for 'chain 'H' and resid 110 through 113' Processing helix chain 'H' and resid 119 through 139 removed outlier: 3.976A pdb=" N ASP H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP H 132 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 160 Processing helix chain 'H' and resid 164 through 183 removed outlier: 4.030A pdb=" N ARG H 167 " --> pdb=" O ALA H 164 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER H 169 " --> pdb=" O SER H 166 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER H 170 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N CYS H 173 " --> pdb=" O SER H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 211 No H-bonds generated for 'chain 'H' and resid 209 through 211' Processing helix chain 'H' and resid 262 through 285 removed outlier: 3.752A pdb=" N GLU H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU H 285 " --> pdb=" O ASP H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 306 Processing helix chain 'H' and resid 317 through 327 Processing helix chain 'H' and resid 335 through 337 No H-bonds generated for 'chain 'H' and resid 335 through 337' Processing helix chain 'H' and resid 381 through 403 Processing helix chain 'H' and resid 413 through 428 removed outlier: 3.893A pdb=" N LYS H 427 " --> pdb=" O THR H 423 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA H 428 " --> pdb=" O GLU H 424 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 455 removed outlier: 3.526A pdb=" N TRP H 435 " --> pdb=" O VAL H 432 " (cutoff:3.500A) Proline residue: H 436 - end of helix removed outlier: 3.922A pdb=" N VAL H 440 " --> pdb=" O TYR H 437 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU H 445 " --> pdb=" O GLN H 442 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL H 446 " --> pdb=" O ALA H 443 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE H 447 " --> pdb=" O LEU H 444 " (cutoff:3.500A) Proline residue: H 448 - end of helix Processing helix chain 'H' and resid 459 through 470 removed outlier: 3.769A pdb=" N THR H 464 " --> pdb=" O ILE H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 493 No H-bonds generated for 'chain 'H' and resid 490 through 493' Processing helix chain 'H' and resid 499 through 518 removed outlier: 3.774A pdb=" N ARG H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 7 removed outlier: 3.754A pdb=" N LEU I 7 " --> pdb=" O ALA I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 7' Processing helix chain 'I' and resid 16 through 37 removed outlier: 3.640A pdb=" N LEU I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN I 37 " --> pdb=" O VAL I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 72 through 87 Processing helix chain 'I' and resid 92 through 112 removed outlier: 3.675A pdb=" N VAL I 96 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU I 112 " --> pdb=" O LEU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 137 removed outlier: 3.625A pdb=" N GLU I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 156 Processing helix chain 'I' and resid 162 through 178 removed outlier: 3.634A pdb=" N VAL I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'I' and resid 253 through 281 removed outlier: 4.642A pdb=" N ARG I 264 " --> pdb=" O VAL I 260 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS I 265 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE I 266 " --> pdb=" O ALA I 262 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE I 267 " --> pdb=" O GLU I 263 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 308 removed outlier: 4.031A pdb=" N GLU I 308 " --> pdb=" O ALA I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.991A pdb=" N GLU I 322 " --> pdb=" O ARG I 318 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR I 325 " --> pdb=" O MET I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 343 No H-bonds generated for 'chain 'I' and resid 341 through 343' Processing helix chain 'I' and resid 381 through 403 Processing helix chain 'I' and resid 413 through 428 Proline residue: I 427 - end of helix Processing helix chain 'I' and resid 433 through 455 removed outlier: 4.212A pdb=" N ILE I 446 " --> pdb=" O ASP I 442 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE I 447 " --> pdb=" O ALA I 443 " (cutoff:3.500A) Proline residue: I 448 - end of helix Processing helix chain 'I' and resid 459 through 468 Processing helix chain 'I' and resid 489 through 492 No H-bonds generated for 'chain 'I' and resid 489 through 492' Processing helix chain 'I' and resid 498 through 517 removed outlier: 3.682A pdb=" N LEU I 517 " --> pdb=" O THR I 513 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 63 through 66 removed outlier: 8.756A pdb=" N ILE A 64 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS A 6 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL A 66 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLN A 8 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A 132 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 7 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN A 134 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA A 9 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR A 136 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN A 165 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N HIS A 137 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE A 167 " --> pdb=" O HIS A 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 51 through 53 Processing sheet with id= C, first strand: chain 'B' and resid 20 through 22 Processing sheet with id= D, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= E, first strand: chain 'B' and resid 202 through 208 removed outlier: 6.703A pdb=" N SER B 373 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N CYS B 205 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE B 375 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE B 207 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU B 377 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 220 through 223 Processing sheet with id= G, first strand: chain 'B' and resid 345 through 347 removed outlier: 6.531A pdb=" N VAL B 290 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR B 242 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 292 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET B 311 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR B 293 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 313 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 408 through 410 Processing sheet with id= I, first strand: chain 'B' and resid 478 through 480 Processing sheet with id= J, first strand: chain 'C' and resid 14 through 17 Processing sheet with id= K, first strand: chain 'C' and resid 47 through 50 Processing sheet with id= L, first strand: chain 'C' and resid 195 through 199 removed outlier: 7.038A pdb=" N CYS C 370 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS C 198 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE C 372 " --> pdb=" O LYS C 198 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 213 through 217 Processing sheet with id= N, first strand: chain 'C' and resid 237 through 240 removed outlier: 6.578A pdb=" N VAL C 288 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU C 240 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 290 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE C 309 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N SER C 291 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA C 311 " --> pdb=" O SER C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 405 through 407 Processing sheet with id= P, first strand: chain 'C' and resid 486 through 489 Processing sheet with id= Q, first strand: chain 'D' and resid 25 through 29 Processing sheet with id= R, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= S, first strand: chain 'D' and resid 209 through 215 removed outlier: 6.905A pdb=" N VAL D 383 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLU D 212 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE D 385 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS D 214 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 387 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 228 through 230 Processing sheet with id= U, first strand: chain 'D' and resid 354 through 356 removed outlier: 6.813A pdb=" N LEU D 299 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU D 251 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE D 301 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N CYS D 302 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 322 " --> pdb=" O CYS D 302 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 418 through 420 Processing sheet with id= W, first strand: chain 'E' and resid 17 through 19 Processing sheet with id= X, first strand: chain 'E' and resid 50 through 53 Processing sheet with id= Y, first strand: chain 'E' and resid 199 through 205 removed outlier: 6.625A pdb=" N CYS E 371 " --> pdb=" O HIS E 200 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE E 202 " --> pdb=" O CYS E 371 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE E 373 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LYS E 204 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU E 375 " --> pdb=" O LYS E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 218 through 220 Processing sheet with id= AA, first strand: chain 'E' and resid 344 through 346 removed outlier: 3.594A pdb=" N ILE E 237 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS E 346 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N CYS E 289 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA E 240 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE E 291 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET E 310 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASN E 292 " --> pdb=" O MET E 310 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE E 312 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 406 through 408 Processing sheet with id= AC, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AD, first strand: chain 'F' and resid 59 through 62 Processing sheet with id= AE, first strand: chain 'F' and resid 208 through 212 removed outlier: 7.046A pdb=" N VAL F 386 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL F 211 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE F 388 " --> pdb=" O VAL F 211 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 226 through 229 Processing sheet with id= AG, first strand: chain 'F' and resid 357 through 359 removed outlier: 6.585A pdb=" N VAL F 297 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE F 249 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU F 299 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N MET F 323 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE F 300 " --> pdb=" O MET F 323 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE F 325 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 421 through 423 Processing sheet with id= AI, first strand: chain 'F' and resid 491 through 494 Processing sheet with id= AJ, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= AK, first strand: chain 'G' and resid 43 through 46 Processing sheet with id= AL, first strand: chain 'G' and resid 196 through 199 removed outlier: 3.946A pdb=" N ASN G 196 " --> pdb=" O ALA G 373 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 213 through 216 Processing sheet with id= AN, first strand: chain 'G' and resid 346 through 348 removed outlier: 6.627A pdb=" N VAL G 285 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU G 237 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 287 " --> pdb=" O LEU G 237 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET G 306 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N THR G 288 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL G 308 " --> pdb=" O THR G 288 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 408 through 410 Processing sheet with id= AP, first strand: chain 'H' and resid 15 through 18 Processing sheet with id= AQ, first strand: chain 'H' and resid 48 through 51 Processing sheet with id= AR, first strand: chain 'H' and resid 199 through 205 removed outlier: 6.539A pdb=" N CYS H 372 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLU H 202 " --> pdb=" O CYS H 372 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE H 374 " --> pdb=" O GLU H 202 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE H 204 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU H 376 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR H 373 " --> pdb=" O LEU H 215 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 218 through 220 Processing sheet with id= AT, first strand: chain 'H' and resid 238 through 241 removed outlier: 6.354A pdb=" N VAL H 289 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU H 241 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE H 291 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR H 310 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR H 292 " --> pdb=" O THR H 310 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE H 312 " --> pdb=" O THR H 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'H' and resid 407 through 409 Processing sheet with id= AV, first strand: chain 'H' and resid 478 through 481 removed outlier: 3.882A pdb=" N THR H 486 " --> pdb=" O ASN H 481 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'I' and resid 12 through 14 Processing sheet with id= AX, first strand: chain 'I' and resid 45 through 48 Processing sheet with id= AY, first strand: chain 'I' and resid 191 through 196 removed outlier: 7.250A pdb=" N VAL I 372 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N MET I 194 " --> pdb=" O VAL I 372 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU I 374 " --> pdb=" O MET I 194 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N MET I 196 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE I 376 " --> pdb=" O MET I 196 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'I' and resid 210 through 212 Processing sheet with id= BA, first strand: chain 'I' and resid 345 through 347 removed outlier: 6.399A pdb=" N GLY I 288 " --> pdb=" O TYR I 229 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU I 231 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL I 290 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N CYS I 233 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE I 292 " --> pdb=" O CYS I 233 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 407 through 409 Processing sheet with id= BC, first strand: chain 'I' and resid 477 through 479 1629 hydrogen bonds defined for protein. 4389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.80 Time building geometry restraints manager: 15.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5881 1.28 - 1.41: 7046 1.41 - 1.55: 20787 1.55 - 1.69: 38 1.69 - 1.82: 350 Bond restraints: 34102 Sorted by residual: bond pdb=" F2 AF3 F 603 " pdb="AL AF3 F 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F3 AF3 E 603 " pdb="AL AF3 E 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" F3 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" F1 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" F1 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 ... (remaining 34097 not shown) Histogram of bond angle deviations from ideal: 97.39 - 105.21: 533 105.21 - 113.03: 19441 113.03 - 120.85: 15805 120.85 - 128.67: 10118 128.67 - 136.49: 155 Bond angle restraints: 46052 Sorted by residual: angle pdb=" CA ASP E 66 " pdb=" CB ASP E 66 " pdb=" CG ASP E 66 " ideal model delta sigma weight residual 112.60 120.65 -8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" CA ASP E 245 " pdb=" CB ASP E 245 " pdb=" CG ASP E 245 " ideal model delta sigma weight residual 112.60 119.70 -7.10 1.00e+00 1.00e+00 5.04e+01 angle pdb=" C ASP G 57 " pdb=" N GLY G 58 " pdb=" CA GLY G 58 " ideal model delta sigma weight residual 119.98 126.99 -7.01 1.11e+00 8.12e-01 3.98e+01 angle pdb=" N THR E 246 " pdb=" CA THR E 246 " pdb=" C THR E 246 " ideal model delta sigma weight residual 111.90 103.80 8.10 1.32e+00 5.74e-01 3.77e+01 angle pdb=" C ASP E 66 " pdb=" CA ASP E 66 " pdb=" CB ASP E 66 " ideal model delta sigma weight residual 109.54 119.96 -10.42 1.84e+00 2.95e-01 3.20e+01 ... (remaining 46047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 20564 35.73 - 71.46: 444 71.46 - 107.19: 42 107.19 - 142.92: 4 142.92 - 178.65: 4 Dihedral angle restraints: 21058 sinusoidal: 8479 harmonic: 12579 Sorted by residual: dihedral pdb=" O1B ADP G 602 " pdb=" O3A ADP G 602 " pdb=" PB ADP G 602 " pdb=" PA ADP G 602 " ideal model delta sinusoidal sigma weight residual -60.00 118.65 -178.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP E 602 " pdb=" O3A ADP E 602 " pdb=" PB ADP E 602 " pdb=" PA ADP E 602 " ideal model delta sinusoidal sigma weight residual 300.00 126.13 173.86 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PA ADP F 602 " pdb=" PB ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 111.18 -171.18 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 21055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 5326 0.111 - 0.223: 149 0.223 - 0.334: 1 0.334 - 0.446: 0 0.446 - 0.557: 1 Chirality restraints: 5477 Sorted by residual: chirality pdb=" CA ASP E 66 " pdb=" N ASP E 66 " pdb=" C ASP E 66 " pdb=" CB ASP E 66 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CA ASP E 245 " pdb=" N ASP E 245 " pdb=" C ASP E 245 " pdb=" CB ASP E 245 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C3' ADP F 602 " pdb=" C2' ADP F 602 " pdb=" C4' ADP F 602 " pdb=" O3' ADP F 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5474 not shown) Planarity restraints: 5885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 468 " 0.022 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C HIS C 468 " -0.072 2.00e-02 2.50e+03 pdb=" O HIS C 468 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA C 469 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 57 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C ASP G 57 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP G 57 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY G 58 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP E 602 " 0.031 2.00e-02 2.50e+03 1.50e-02 6.22e+00 pdb=" C2 ADP E 602 " -0.003 2.00e-02 2.50e+03 pdb=" C4 ADP E 602 " -0.013 2.00e-02 2.50e+03 pdb=" C5 ADP E 602 " -0.013 2.00e-02 2.50e+03 pdb=" C6 ADP E 602 " -0.009 2.00e-02 2.50e+03 pdb=" C8 ADP E 602 " 0.003 2.00e-02 2.50e+03 pdb=" N1 ADP E 602 " 0.015 2.00e-02 2.50e+03 pdb=" N3 ADP E 602 " -0.011 2.00e-02 2.50e+03 pdb=" N6 ADP E 602 " 0.022 2.00e-02 2.50e+03 pdb=" N7 ADP E 602 " -0.011 2.00e-02 2.50e+03 pdb=" N9 ADP E 602 " -0.011 2.00e-02 2.50e+03 ... (remaining 5882 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 149 2.53 - 3.12: 24744 3.12 - 3.71: 49050 3.71 - 4.31: 67808 4.31 - 4.90: 119387 Nonbonded interactions: 261138 Sorted by model distance: nonbonded pdb="MG MG C 601 " pdb=" O3A ADP C 602 " model vdw 1.932 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1B ADP D 602 " model vdw 1.946 2.170 nonbonded pdb="MG MG B 601 " pdb=" F1 AF3 B 603 " model vdw 1.955 2.120 nonbonded pdb="MG MG I 601 " pdb=" F1 AF3 I 603 " model vdw 1.971 2.120 nonbonded pdb="MG MG B 601 " pdb=" O1B ADP B 602 " model vdw 1.994 2.170 ... (remaining 261133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.130 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 88.390 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.005 0.164 34102 Z= 0.351 Angle : 0.678 11.561 46052 Z= 0.366 Chirality : 0.044 0.557 5477 Planarity : 0.004 0.045 5885 Dihedral : 15.522 178.654 12916 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 0.19 % Allowed : 9.48 % Favored : 90.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.13), residues: 4353 helix: 2.20 (0.11), residues: 2205 sheet: 0.70 (0.22), residues: 592 loop : -1.18 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS A 137 PHE 0.024 0.001 PHE G 8 TYR 0.011 0.001 TYR G 131 ARG 0.009 0.000 ARG C 535 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 247 time to evaluate : 4.162 Fit side-chains REVERT: A 42 LEU cc_start: 0.7751 (mm) cc_final: 0.7141 (tt) REVERT: C 252 ASN cc_start: 0.7651 (t0) cc_final: 0.7088 (t0) REVERT: C 470 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7308 (pt0) REVERT: E 48 MET cc_start: 0.8897 (mmm) cc_final: 0.8681 (mmt) REVERT: G 225 MET cc_start: 0.9550 (mtt) cc_final: 0.9331 (mtt) REVERT: G 430 MET cc_start: 0.7023 (mmm) cc_final: 0.6786 (mmm) REVERT: H 182 MET cc_start: 0.8808 (ttm) cc_final: 0.8608 (ptm) outliers start: 7 outliers final: 1 residues processed: 250 average time/residue: 1.4432 time to fit residues: 433.2133 Evaluate side-chains 222 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 470 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 8.9990 chunk 328 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 340 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 206 optimal weight: 0.0770 chunk 253 optimal weight: 8.9990 chunk 394 optimal weight: 8.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 134 GLN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 HIS H 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34102 Z= 0.216 Angle : 0.566 8.038 46052 Z= 0.280 Chirality : 0.043 0.172 5477 Planarity : 0.004 0.057 5885 Dihedral : 8.115 177.430 4741 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.43 % Allowed : 10.80 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.13), residues: 4353 helix: 2.17 (0.11), residues: 2193 sheet: 0.86 (0.22), residues: 592 loop : -1.10 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.009 0.001 HIS H 111 PHE 0.018 0.001 PHE G 8 TYR 0.016 0.001 TYR A 50 ARG 0.006 0.000 ARG C 535 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 238 time to evaluate : 4.118 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8207 (mp) REVERT: C 252 ASN cc_start: 0.7674 (t0) cc_final: 0.7095 (t0) REVERT: C 470 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6842 (pt0) REVERT: D 39 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7995 (mtm) REVERT: D 290 GLN cc_start: 0.8008 (tp40) cc_final: 0.7577 (tp-100) REVERT: E 445 MET cc_start: 0.9147 (mmt) cc_final: 0.8835 (tpp) REVERT: F 399 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: F 458 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8395 (mtp) REVERT: G 156 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8517 (mtm) REVERT: G 225 MET cc_start: 0.9567 (mtt) cc_final: 0.9330 (mtt) outliers start: 52 outliers final: 18 residues processed: 273 average time/residue: 1.3498 time to fit residues: 447.7618 Evaluate side-chains 243 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 470 GLN Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 381 ASN Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 394 optimal weight: 8.9990 chunk 426 optimal weight: 0.0570 chunk 351 optimal weight: 10.0000 chunk 391 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 134 GLN D 278 GLN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34102 Z= 0.211 Angle : 0.551 9.576 46052 Z= 0.272 Chirality : 0.042 0.177 5477 Planarity : 0.004 0.047 5885 Dihedral : 7.649 176.546 4739 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 1.56 % Allowed : 11.87 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.13), residues: 4353 helix: 2.10 (0.11), residues: 2196 sheet: 0.85 (0.22), residues: 610 loop : -1.09 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.009 0.001 HIS H 111 PHE 0.015 0.001 PHE G 167 TYR 0.013 0.001 TYR A 50 ARG 0.005 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 234 time to evaluate : 3.960 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8237 (mp) REVERT: A 73 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5838 (mpp) REVERT: C 153 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7930 (mtmm) REVERT: C 185 MET cc_start: 0.8028 (mtm) cc_final: 0.7823 (mtp) REVERT: C 252 ASN cc_start: 0.7713 (t0) cc_final: 0.7096 (t0) REVERT: C 512 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8530 (t0) REVERT: D 39 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7993 (mtm) REVERT: D 290 GLN cc_start: 0.8024 (tp-100) cc_final: 0.7630 (tp-100) REVERT: F 27 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6481 (mmp-170) REVERT: F 399 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: F 458 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8410 (mtp) REVERT: G 156 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8515 (mtm) REVERT: G 302 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: G 430 MET cc_start: 0.7144 (mmm) cc_final: 0.6791 (mmm) REVERT: I 44 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8882 (mmt) outliers start: 57 outliers final: 25 residues processed: 272 average time/residue: 1.4140 time to fit residues: 464.0832 Evaluate side-chains 258 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 223 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 8.9990 chunk 296 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 396 optimal weight: 10.0000 chunk 419 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 375 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 134 GLN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN G 366 ASN ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34102 Z= 0.268 Angle : 0.575 9.702 46052 Z= 0.285 Chirality : 0.044 0.201 5477 Planarity : 0.004 0.043 5885 Dihedral : 7.346 166.262 4736 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 1.84 % Allowed : 12.61 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.13), residues: 4353 helix: 1.91 (0.11), residues: 2212 sheet: 0.82 (0.22), residues: 594 loop : -1.18 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.008 0.001 HIS H 111 PHE 0.017 0.001 PHE G 167 TYR 0.012 0.001 TYR B 505 ARG 0.009 0.000 ARG H 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 230 time to evaluate : 4.033 Fit side-chains revert: symmetry clash REVERT: C 252 ASN cc_start: 0.7712 (t0) cc_final: 0.7103 (t0) REVERT: C 512 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8556 (t0) REVERT: D 39 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8026 (mtm) REVERT: D 290 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7799 (tp-100) REVERT: F 399 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: G 156 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8539 (mtm) REVERT: G 302 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: G 430 MET cc_start: 0.7214 (mmm) cc_final: 0.6877 (mmm) outliers start: 67 outliers final: 31 residues processed: 279 average time/residue: 1.3544 time to fit residues: 459.3528 Evaluate side-chains 252 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 0.6980 chunk 238 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 312 optimal weight: 1.9990 chunk 173 optimal weight: 0.3980 chunk 357 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 4.9990 chunk 376 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 8 GLN A 89 ASN A 134 GLN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34102 Z= 0.145 Angle : 0.516 9.467 46052 Z= 0.253 Chirality : 0.041 0.177 5477 Planarity : 0.003 0.038 5885 Dihedral : 6.944 159.492 4736 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.59 % Allowed : 13.70 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4353 helix: 2.13 (0.11), residues: 2201 sheet: 0.87 (0.22), residues: 602 loop : -1.08 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.007 0.001 HIS H 111 PHE 0.013 0.001 PHE G 167 TYR 0.012 0.001 TYR B 505 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 232 time to evaluate : 4.314 Fit side-chains revert: symmetry clash REVERT: B 315 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8353 (pp) REVERT: C 251 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8224 (p0) REVERT: C 512 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8443 (t0) REVERT: D 81 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7857 (ttm) REVERT: D 290 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7825 (tp-100) REVERT: F 399 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: G 156 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8425 (mtm) REVERT: G 302 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: G 409 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8773 (m) REVERT: G 430 MET cc_start: 0.7190 (mmm) cc_final: 0.6835 (mmm) REVERT: I 321 MET cc_start: 0.8998 (mmp) cc_final: 0.8721 (mmp) outliers start: 58 outliers final: 19 residues processed: 275 average time/residue: 1.3144 time to fit residues: 438.3537 Evaluate side-chains 246 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 219 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 9.9990 chunk 377 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 419 optimal weight: 5.9990 chunk 348 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 8 GLN A 134 GLN B 471 HIS ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 34102 Z= 0.456 Angle : 0.670 12.501 46052 Z= 0.335 Chirality : 0.048 0.193 5477 Planarity : 0.004 0.048 5885 Dihedral : 7.430 152.885 4736 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.66 % Favored : 95.31 % Rotamer: Outliers : 2.22 % Allowed : 14.28 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.13), residues: 4353 helix: 1.66 (0.11), residues: 2201 sheet: 0.68 (0.22), residues: 597 loop : -1.30 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 485 HIS 0.008 0.001 HIS I 470 PHE 0.026 0.002 PHE D 16 TYR 0.014 0.002 TYR D 420 ARG 0.006 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 229 time to evaluate : 4.158 Fit side-chains revert: symmetry clash REVERT: B 315 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8717 (pp) REVERT: C 512 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8643 (t0) REVERT: D 81 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7968 (ttm) REVERT: D 290 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7876 (tp-100) REVERT: G 156 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8635 (mtm) REVERT: G 182 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7261 (t) REVERT: G 409 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8679 (m) REVERT: G 430 MET cc_start: 0.7268 (mmm) cc_final: 0.6964 (mmm) REVERT: H 7 VAL cc_start: 0.7219 (t) cc_final: 0.6987 (p) REVERT: H 15 LYS cc_start: 0.7739 (tttp) cc_final: 0.7271 (mmmt) REVERT: H 291 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8813 (mm) REVERT: I 426 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8399 (pttm) outliers start: 81 outliers final: 38 residues processed: 291 average time/residue: 1.3859 time to fit residues: 487.1003 Evaluate side-chains 262 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 216 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 426 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 chunk 306 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 353 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 418 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 134 GLN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34102 Z= 0.331 Angle : 0.607 11.862 46052 Z= 0.303 Chirality : 0.045 0.186 5477 Planarity : 0.004 0.043 5885 Dihedral : 7.301 151.127 4736 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 1.95 % Allowed : 14.99 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.13), residues: 4353 helix: 1.69 (0.11), residues: 2187 sheet: 0.66 (0.22), residues: 595 loop : -1.31 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.006 0.001 HIS I 470 PHE 0.030 0.002 PHE A 20 TYR 0.014 0.001 TYR B 505 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 222 time to evaluate : 4.453 Fit side-chains revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7597 (tm) REVERT: B 315 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8755 (pp) REVERT: C 512 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8606 (t0) REVERT: D 81 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7923 (ttm) REVERT: D 290 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7885 (tp-100) REVERT: E 312 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8757 (mm) REVERT: F 399 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: G 156 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8537 (mtm) REVERT: G 430 MET cc_start: 0.7275 (mmm) cc_final: 0.6942 (mmm) REVERT: H 7 VAL cc_start: 0.7197 (t) cc_final: 0.6950 (p) REVERT: H 15 LYS cc_start: 0.7636 (tttp) cc_final: 0.7399 (tttt) REVERT: H 291 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8787 (mm) REVERT: I 190 MET cc_start: 0.8821 (mmp) cc_final: 0.8584 (mmp) REVERT: I 426 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8388 (pttm) outliers start: 71 outliers final: 38 residues processed: 277 average time/residue: 1.3989 time to fit residues: 471.8819 Evaluate side-chains 262 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 215 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 492 GLU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 426 LYS Chi-restraints excluded: chain I residue 514 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 284 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 328 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 134 GLN B 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34102 Z= 0.168 Angle : 0.532 11.878 46052 Z= 0.263 Chirality : 0.042 0.178 5477 Planarity : 0.003 0.041 5885 Dihedral : 6.917 147.439 4736 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.45 % Allowed : 15.62 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 4353 helix: 2.00 (0.11), residues: 2180 sheet: 0.74 (0.22), residues: 599 loop : -1.18 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.003 0.001 HIS I 470 PHE 0.018 0.001 PHE A 20 TYR 0.012 0.001 TYR B 505 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 230 time to evaluate : 3.510 Fit side-chains revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7208 (tt) REVERT: C 153 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7872 (mttp) REVERT: C 512 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8500 (t0) REVERT: D 81 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7907 (ttm) REVERT: D 290 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7889 (tp-100) REVERT: F 399 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: G 156 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8421 (mtm) REVERT: G 182 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7515 (t) REVERT: G 430 MET cc_start: 0.7229 (mmm) cc_final: 0.6908 (mmm) REVERT: H 7 VAL cc_start: 0.7120 (t) cc_final: 0.6898 (p) REVERT: H 15 LYS cc_start: 0.7608 (tttp) cc_final: 0.7228 (mmmt) REVERT: I 190 MET cc_start: 0.8797 (mmp) cc_final: 0.8564 (mmp) REVERT: I 426 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8346 (pttm) outliers start: 53 outliers final: 32 residues processed: 272 average time/residue: 1.4302 time to fit residues: 468.4063 Evaluate side-chains 255 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 216 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 426 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 380 optimal weight: 2.9990 chunk 400 optimal weight: 0.9990 chunk 365 optimal weight: 9.9990 chunk 389 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 306 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 368 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 11 GLN A 14 ASN D 515 GLN H 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 34102 Z= 0.132 Angle : 0.509 12.533 46052 Z= 0.250 Chirality : 0.041 0.188 5477 Planarity : 0.003 0.038 5885 Dihedral : 6.644 155.664 4736 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.12 % Allowed : 16.28 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.13), residues: 4353 helix: 2.20 (0.11), residues: 2178 sheet: 0.87 (0.22), residues: 596 loop : -1.01 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 21 HIS 0.005 0.000 HIS A 6 PHE 0.027 0.001 PHE A 20 TYR 0.013 0.001 TYR B 501 ARG 0.008 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 240 time to evaluate : 3.518 Fit side-chains revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7233 (tt) REVERT: D 81 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7855 (ttm) REVERT: G 156 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8409 (mtm) REVERT: G 182 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7536 (t) REVERT: G 430 MET cc_start: 0.7218 (mmm) cc_final: 0.6894 (mmm) REVERT: H 7 VAL cc_start: 0.7228 (t) cc_final: 0.7012 (p) REVERT: I 190 MET cc_start: 0.8669 (mmp) cc_final: 0.8464 (mmp) outliers start: 41 outliers final: 24 residues processed: 273 average time/residue: 1.3670 time to fit residues: 452.3068 Evaluate side-chains 255 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 227 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 0.7980 chunk 412 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 195 optimal weight: 7.9990 chunk 286 optimal weight: 9.9990 chunk 432 optimal weight: 1.9990 chunk 397 optimal weight: 1.9990 chunk 344 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 14 ASN E 294 GLN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34102 Z= 0.286 Angle : 0.582 12.374 46052 Z= 0.289 Chirality : 0.044 0.180 5477 Planarity : 0.004 0.039 5885 Dihedral : 6.878 155.713 4736 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.02 % Favored : 95.96 % Rotamer: Outliers : 1.18 % Allowed : 16.39 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.13), residues: 4353 helix: 1.98 (0.11), residues: 2188 sheet: 0.82 (0.22), residues: 595 loop : -1.11 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 485 HIS 0.005 0.001 HIS I 382 PHE 0.021 0.002 PHE G 8 TYR 0.014 0.001 TYR G 181 ARG 0.007 0.000 ARG A 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7605 (tm) REVERT: C 153 LYS cc_start: 0.8211 (mttp) cc_final: 0.7942 (mttp) REVERT: D 81 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7959 (ttm) REVERT: G 156 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8463 (mtm) REVERT: G 182 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7531 (t) REVERT: G 430 MET cc_start: 0.7234 (mmm) cc_final: 0.6887 (mmm) REVERT: H 7 VAL cc_start: 0.7195 (t) cc_final: 0.6942 (p) REVERT: I 190 MET cc_start: 0.8820 (mmp) cc_final: 0.8606 (mmp) outliers start: 43 outliers final: 25 residues processed: 261 average time/residue: 1.3772 time to fit residues: 437.0893 Evaluate side-chains 249 residues out of total 3649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 4.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 273 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 317 optimal weight: 1.9990 chunk 50 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 344 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 354 optimal weight: 0.3980 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 14 ASN B 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.076162 restraints weight = 60623.550| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.54 r_work: 0.2913 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34102 Z= 0.218 Angle : 0.553 12.325 46052 Z= 0.274 Chirality : 0.042 0.182 5477 Planarity : 0.003 0.040 5885 Dihedral : 6.801 153.703 4736 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.12 % Allowed : 16.47 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.13), residues: 4353 helix: 1.99 (0.11), residues: 2187 sheet: 0.87 (0.22), residues: 589 loop : -1.09 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.003 0.001 HIS I 470 PHE 0.025 0.001 PHE A 20 TYR 0.014 0.001 TYR G 181 ARG 0.007 0.000 ARG A 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8735.81 seconds wall clock time: 156 minutes 33.90 seconds (9393.90 seconds total)