Starting phenix.real_space_refine on Wed Jan 17 17:00:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/01_2024/1oed_1044.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/01_2024/1oed_1044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/01_2024/1oed_1044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/01_2024/1oed_1044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/01_2024/1oed_1044.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/01_2024/1oed_1044.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3331 2.51 5 N 735 2.21 5 O 823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "C PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "E PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4926 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 978 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 982 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 1 Chain: "D" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 978 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Time building chain proxies: 3.18, per 1000 atoms: 0.65 Number of scatterers: 4926 At special positions: 0 Unit cell: (96, 88, 67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 823 8.00 N 735 7.00 C 3331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 883.4 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 212 through 239 removed outlier: 3.584A pdb=" N VAL A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Proline residue: A 221 - end of helix Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 242 through 271 removed outlier: 3.660A pdb=" N GLU A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 275 through 302 removed outlier: 3.935A pdb=" N PHE A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 437 Processing helix chain 'B' and resid 218 through 245 removed outlier: 3.668A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Proline residue: B 227 - end of helix Proline residue: B 242 - end of helix Processing helix chain 'B' and resid 248 through 277 removed outlier: 3.500A pdb=" N ALA B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Proline residue: B 271 - end of helix removed outlier: 3.781A pdb=" N LEU B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 307 removed outlier: 4.130A pdb=" N ILE B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 462 Processing helix chain 'C' and resid 226 through 253 removed outlier: 4.092A pdb=" N ASN C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Proline residue: C 235 - end of helix Proline residue: C 250 - end of helix Processing helix chain 'C' and resid 256 through 285 Proline residue: C 279 - end of helix Processing helix chain 'C' and resid 289 through 316 removed outlier: 3.916A pdb=" N PHE C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 484 Proline residue: C 463 - end of helix Proline residue: C 481 - end of helix Processing helix chain 'D' and resid 212 through 239 removed outlier: 3.582A pdb=" N VAL D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Proline residue: D 221 - end of helix Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 242 through 271 removed outlier: 3.660A pdb=" N GLU D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Proline residue: D 265 - end of helix Processing helix chain 'D' and resid 275 through 302 removed outlier: 3.936A pdb=" N PHE D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR D 281 " --> pdb=" O TYR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 437 Processing helix chain 'E' and resid 221 through 246 Proline residue: E 229 - end of helix removed outlier: 3.979A pdb=" N SER E 234 " --> pdb=" O CYS E 230 " (cutoff:3.500A) Proline residue: E 244 - end of helix Processing helix chain 'E' and resid 250 through 280 Proline residue: E 274 - end of helix Processing helix chain 'E' and resid 285 through 311 Processing helix chain 'E' and resid 445 through 478 Proline residue: E 476 - end of helix 435 hydrogen bonds defined for protein. 1305 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: 1.31 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 751 1.31 - 1.43: 1242 1.43 - 1.56: 2970 1.56 - 1.69: 6 1.69 - 1.82: 61 Bond restraints: 5030 Sorted by residual: bond pdb=" N PRO B 271 " pdb=" CD PRO B 271 " ideal model delta sigma weight residual 1.473 1.221 0.252 1.40e-02 5.10e+03 3.23e+02 bond pdb=" C ALA A 403 " pdb=" O ALA A 403 " ideal model delta sigma weight residual 1.231 1.384 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C ALA D 403 " pdb=" O ALA D 403 " ideal model delta sigma weight residual 1.231 1.384 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" CB VAL B 445 " pdb=" CG1 VAL B 445 " ideal model delta sigma weight residual 1.521 1.721 -0.200 3.30e-02 9.18e+02 3.69e+01 bond pdb=" N PRO B 464 " pdb=" CD PRO B 464 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.92e+01 ... (remaining 5025 not shown) Histogram of bond angle deviations from ideal: 97.12 - 104.51: 82 104.51 - 111.91: 2592 111.91 - 119.31: 1609 119.31 - 126.71: 2488 126.71 - 134.10: 84 Bond angle restraints: 6855 Sorted by residual: angle pdb=" OE1 GLN E 474 " pdb=" CD GLN E 474 " pdb=" NE2 GLN E 474 " ideal model delta sigma weight residual 122.60 112.76 9.84 1.00e+00 1.00e+00 9.69e+01 angle pdb=" OE1 GLN A 435 " pdb=" CD GLN A 435 " pdb=" NE2 GLN A 435 " ideal model delta sigma weight residual 122.60 112.77 9.83 1.00e+00 1.00e+00 9.67e+01 angle pdb=" OE1 GLN E 262 " pdb=" CD GLN E 262 " pdb=" NE2 GLN E 262 " ideal model delta sigma weight residual 122.60 112.81 9.79 1.00e+00 1.00e+00 9.59e+01 angle pdb=" OE1 GLN E 246 " pdb=" CD GLN E 246 " pdb=" NE2 GLN E 246 " ideal model delta sigma weight residual 122.60 112.84 9.76 1.00e+00 1.00e+00 9.52e+01 angle pdb=" CA THR C 462 " pdb=" C THR C 462 " pdb=" N PRO C 463 " ideal model delta sigma weight residual 120.77 111.31 9.46 9.70e-01 1.06e+00 9.51e+01 ... (remaining 6850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2582 17.92 - 35.83: 266 35.83 - 53.75: 111 53.75 - 71.67: 12 71.67 - 89.59: 4 Dihedral angle restraints: 2975 sinusoidal: 1114 harmonic: 1861 Sorted by residual: dihedral pdb=" C PRO E 476 " pdb=" N PRO E 476 " pdb=" CA PRO E 476 " pdb=" CB PRO E 476 " ideal model delta harmonic sigma weight residual -120.70 -109.72 -10.98 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" C PRO D 236 " pdb=" N PRO D 236 " pdb=" CA PRO D 236 " pdb=" CB PRO D 236 " ideal model delta harmonic sigma weight residual -120.70 -109.89 -10.81 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" C PRO A 236 " pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" CB PRO A 236 " ideal model delta harmonic sigma weight residual -120.70 -109.91 -10.79 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 2972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 898 0.276 - 0.552: 5 0.552 - 0.827: 0 0.827 - 1.103: 0 1.103 - 1.379: 1 Chirality restraints: 904 Sorted by residual: chirality pdb=" CB VAL B 445 " pdb=" CA VAL B 445 " pdb=" CG1 VAL B 445 " pdb=" CG2 VAL B 445 " both_signs ideal model delta sigma weight residual False -2.63 -4.01 1.38 2.00e-01 2.50e+01 4.75e+01 chirality pdb=" CB ILE B 446 " pdb=" CA ILE B 446 " pdb=" CG1 ILE B 446 " pdb=" CG2 ILE B 446 " both_signs ideal model delta sigma weight residual False 2.64 3.17 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" CA HIS E 471 " pdb=" N HIS E 471 " pdb=" C HIS E 471 " pdb=" CB HIS E 471 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 901 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 476 " -0.039 2.00e-02 2.50e+03 8.13e-02 6.62e+01 pdb=" C PRO E 476 " 0.141 2.00e-02 2.50e+03 pdb=" O PRO E 476 " -0.054 2.00e-02 2.50e+03 pdb=" N GLU E 477 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 275 " 0.026 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C LEU B 275 " -0.086 2.00e-02 2.50e+03 pdb=" O LEU B 275 " 0.031 2.00e-02 2.50e+03 pdb=" N SER B 276 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 445 " 0.019 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C LYS E 445 " -0.072 2.00e-02 2.50e+03 pdb=" O LYS E 445 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL E 446 " 0.024 2.00e-02 2.50e+03 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 21 1.93 - 2.67: 595 2.67 - 3.41: 8998 3.41 - 4.16: 13035 4.16 - 4.90: 21585 Nonbonded interactions: 44234 Sorted by model distance: nonbonded pdb=" O TYR E 241 " pdb=" CG PRO E 244 " model vdw 1.183 3.440 nonbonded pdb=" O HIS B 460 " pdb=" CD PRO B 464 " model vdw 1.352 3.440 nonbonded pdb=" O TYR E 241 " pdb=" CD PRO E 244 " model vdw 1.447 3.440 nonbonded pdb=" O PHE B 239 " pdb=" CD PRO B 242 " model vdw 1.624 3.440 nonbonded pdb=" O PHE C 459 " pdb=" CD PRO C 463 " model vdw 1.640 3.440 ... (remaining 44229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.060 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1921 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 : 0.014 0.252 5030 Z= 0.934 Angle : 2.288 13.685 6855 Z= 1.670 Chirality : 0.097 1.379 904 Planarity : 0.009 0.081 798 Dihedral : 17.230 89.585 1757 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 224.94 Ramachandran Plot: Outliers : 2.11 % Allowed : 5.19 % Favored : 92.69 % Rotamer: Outliers : 19.76 % Allowed : 14.04 % Favored : 66.20 % Cbeta Deviations : 0.49 % 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: -3.67 (0.27), residues: 616 helix: -2.15 (0.18), residues: 512 sheet: None (None), residues: 0 loop : -2.61 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.005 TRP E 453 HIS 0.006 0.001 HIS B 460 PHE 0.021 0.002 PHE C 247 TYR 0.014 0.001 TYR B 220 ARG 0.001 0.000 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 111 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.4349 (OUTLIER) cc_final: 0.4004 (m-80) REVERT: A 284 PHE cc_start: 0.2953 (OUTLIER) cc_final: 0.2420 (t80) REVERT: A 411 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.4758 (mm) REVERT: C 457 SER cc_start: -0.6578 (OUTLIER) cc_final: -0.7210 (m) REVERT: C 462 THR cc_start: 0.6349 (m) cc_final: 0.5915 (m) REVERT: C 475 MET cc_start: 0.0883 (OUTLIER) cc_final: -0.0572 (mtt) REVERT: C 479 ASN cc_start: -0.2803 (OUTLIER) cc_final: -0.3292 (t0) REVERT: D 243 MET cc_start: 0.3821 (mtt) cc_final: 0.2367 (pmm) REVERT: D 298 THR cc_start: 0.5185 (OUTLIER) cc_final: 0.4842 (m) REVERT: D 302 SER cc_start: 0.6645 (OUTLIER) cc_final: 0.5667 (t) REVERT: E 272 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.4499 (tttt) REVERT: E 297 ILE cc_start: 0.1827 (OUTLIER) cc_final: 0.1572 (tp) outliers start: 114 outliers final: 46 residues processed: 198 average time/residue: 0.1495 time to fit residues: 38.1042 Evaluate side-chains 128 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 72 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 453 TRP Chi-restraints excluded: chain E residue 463 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 50.0000 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN C 479 ASN D 217 ASN ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2057 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 5030 Z= 0.417 Angle : 1.166 13.426 6855 Z= 0.592 Chirality : 0.056 0.263 904 Planarity : 0.009 0.067 798 Dihedral : 13.687 80.077 764 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 35.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 9.88 % Allowed : 17.16 % Favored : 72.96 % 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: -1.78 (0.32), residues: 616 helix: -0.86 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -2.67 (0.84), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 453 HIS 0.010 0.002 HIS D 300 PHE 0.036 0.004 PHE E 242 TYR 0.038 0.002 TYR C 248 ARG 0.004 0.001 ARG C 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 72 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 THR cc_start: 0.6656 (OUTLIER) cc_final: 0.6435 (p) REVERT: B 281 ILE cc_start: 0.3011 (mm) cc_final: 0.2785 (mm) REVERT: B 440 LEU cc_start: 0.5355 (OUTLIER) cc_final: 0.5135 (tp) REVERT: C 257 MET cc_start: -0.0433 (mtt) cc_final: -0.1065 (mtt) REVERT: C 451 GLN cc_start: 0.3360 (OUTLIER) cc_final: 0.3120 (tp40) REVERT: D 232 VAL cc_start: 0.0070 (OUTLIER) cc_final: -0.0289 (t) REVERT: D 298 THR cc_start: 0.4517 (OUTLIER) cc_final: 0.4316 (m) outliers start: 57 outliers final: 19 residues processed: 113 average time/residue: 0.1403 time to fit residues: 21.0564 Evaluate side-chains 79 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 55 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 453 TRP Chi-restraints excluded: chain E residue 454 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 40.0000 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN C 313 HIS ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2189 moved from start: 0.8238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5030 Z= 0.332 Angle : 0.963 11.076 6855 Z= 0.472 Chirality : 0.049 0.306 904 Planarity : 0.007 0.070 798 Dihedral : 9.859 79.870 688 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 29.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.37 % Allowed : 18.54 % Favored : 76.08 % 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: -0.66 (0.33), residues: 616 helix: -0.10 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.14 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 453 HIS 0.006 0.001 HIS B 306 PHE 0.036 0.003 PHE D 256 TYR 0.008 0.001 TYR E 241 ARG 0.004 0.001 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 67 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 THR cc_start: -0.0452 (OUTLIER) cc_final: -0.0815 (p) REVERT: A 422 THR cc_start: 0.6939 (OUTLIER) cc_final: 0.6492 (m) REVERT: C 257 MET cc_start: -0.1785 (mtt) cc_final: -0.3075 (mmt) REVERT: C 462 THR cc_start: 0.6115 (p) cc_final: 0.5831 (p) REVERT: C 475 MET cc_start: -0.0622 (ptt) cc_final: -0.3470 (mmt) REVERT: D 435 GLN cc_start: -0.2153 (OUTLIER) cc_final: -0.2674 (mt0) REVERT: E 454 ILE cc_start: 0.0169 (OUTLIER) cc_final: -0.0085 (pp) outliers start: 31 outliers final: 13 residues processed: 93 average time/residue: 0.1359 time to fit residues: 17.0910 Evaluate side-chains 75 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 453 TRP Chi-restraints excluded: chain E residue 454 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 50.0000 chunk 6 optimal weight: 0.0980 chunk 26 optimal weight: 40.0000 chunk 36 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2273 moved from start: 0.9511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5030 Z= 0.309 Angle : 0.916 10.331 6855 Z= 0.442 Chirality : 0.046 0.196 904 Planarity : 0.007 0.065 798 Dihedral : 7.996 76.431 670 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.55 % Allowed : 18.89 % Favored : 75.56 % 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: 0.06 (0.33), residues: 616 helix: 0.36 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.71 (0.73), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.003 0.001 HIS A 300 PHE 0.030 0.002 PHE D 256 TYR 0.010 0.001 TYR C 248 ARG 0.008 0.001 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 64 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 MET cc_start: 0.0695 (mtt) cc_final: 0.0414 (mtp) REVERT: C 257 MET cc_start: -0.1818 (mtt) cc_final: -0.3113 (mmt) REVERT: C 475 MET cc_start: -0.0720 (ptt) cc_final: -0.3347 (mmt) REVERT: D 435 GLN cc_start: -0.2591 (OUTLIER) cc_final: -0.2871 (mt0) outliers start: 32 outliers final: 19 residues processed: 92 average time/residue: 0.1169 time to fit residues: 15.0987 Evaluate side-chains 79 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 40.0000 chunk 40 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 overall best weight: 7.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 435 GLN ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2479 moved from start: 1.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5030 Z= 0.305 Angle : 0.889 9.914 6855 Z= 0.433 Chirality : 0.046 0.234 904 Planarity : 0.008 0.067 798 Dihedral : 7.217 65.100 670 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.03 % Allowed : 18.54 % Favored : 76.43 % 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: 0.84 (0.34), residues: 616 helix: 0.84 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -1.26 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 453 HIS 0.007 0.002 HIS B 306 PHE 0.029 0.002 PHE D 256 TYR 0.015 0.002 TYR B 220 ARG 0.003 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 65 time to evaluate : 0.602 Fit side-chains REVERT: C 257 MET cc_start: -0.2222 (mtt) cc_final: -0.2579 (mmt) REVERT: C 460 ILE cc_start: 0.1752 (pt) cc_final: 0.1411 (pt) REVERT: C 475 MET cc_start: 0.0318 (ptt) cc_final: -0.2484 (mmt) outliers start: 29 outliers final: 14 residues processed: 86 average time/residue: 0.1316 time to fit residues: 15.5139 Evaluate side-chains 68 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 0.0020 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 overall best weight: 2.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2473 moved from start: 1.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5030 Z= 0.263 Angle : 0.875 10.509 6855 Z= 0.414 Chirality : 0.043 0.196 904 Planarity : 0.007 0.059 798 Dihedral : 5.904 59.875 660 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.12 % Allowed : 22.18 % Favored : 74.70 % 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: 1.34 (0.34), residues: 616 helix: 1.22 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -1.54 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 453 HIS 0.007 0.001 HIS D 300 PHE 0.026 0.002 PHE D 256 TYR 0.024 0.001 TYR E 286 ARG 0.002 0.000 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.529 Fit side-chains REVERT: B 231 ILE cc_start: 0.1655 (mm) cc_final: 0.1388 (mm) REVERT: C 257 MET cc_start: -0.2097 (mtt) cc_final: -0.2408 (mmt) REVERT: C 460 ILE cc_start: 0.1988 (pt) cc_final: 0.1677 (pt) outliers start: 18 outliers final: 12 residues processed: 74 average time/residue: 0.1297 time to fit residues: 13.4462 Evaluate side-chains 69 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 30.0000 chunk 57 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 39 optimal weight: 40.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN E 225 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2655 moved from start: 1.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5030 Z= 0.291 Angle : 0.882 9.376 6855 Z= 0.430 Chirality : 0.044 0.199 904 Planarity : 0.007 0.059 798 Dihedral : 5.866 58.938 660 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.64 % Allowed : 21.66 % Favored : 74.70 % 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: 1.54 (0.34), residues: 616 helix: 1.38 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.53 (0.73), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.009 0.002 HIS D 300 PHE 0.026 0.002 PHE D 256 TYR 0.014 0.002 TYR B 220 ARG 0.003 0.000 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 MET cc_start: -0.2495 (mtt) cc_final: -0.2823 (mmt) REVERT: C 460 ILE cc_start: 0.2261 (pt) cc_final: 0.1916 (pt) REVERT: D 278 MET cc_start: 0.5218 (ppp) cc_final: 0.4889 (ppp) outliers start: 21 outliers final: 14 residues processed: 81 average time/residue: 0.1268 time to fit residues: 14.2370 Evaluate side-chains 75 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2770 moved from start: 1.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5030 Z= 0.286 Angle : 0.911 10.645 6855 Z= 0.436 Chirality : 0.047 0.346 904 Planarity : 0.007 0.058 798 Dihedral : 5.972 59.605 660 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.81 % Allowed : 21.84 % Favored : 74.35 % 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: 1.66 (0.35), residues: 616 helix: 1.49 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.69 (0.74), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.011 0.002 HIS D 300 PHE 0.023 0.002 PHE C 294 TYR 0.026 0.002 TYR A 213 ARG 0.003 0.001 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 257 MET cc_start: -0.2941 (mtt) cc_final: -0.3433 (mmt) REVERT: C 294 PHE cc_start: 0.2095 (OUTLIER) cc_final: 0.1556 (m-10) REVERT: C 460 ILE cc_start: 0.2252 (pt) cc_final: 0.1921 (pt) REVERT: D 296 ILE cc_start: 0.5854 (pp) cc_final: 0.5612 (pp) outliers start: 22 outliers final: 14 residues processed: 85 average time/residue: 0.1303 time to fit residues: 15.0761 Evaluate side-chains 78 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 40.0000 chunk 53 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 59 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2807 moved from start: 1.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5030 Z= 0.275 Angle : 0.915 12.174 6855 Z= 0.434 Chirality : 0.045 0.317 904 Planarity : 0.007 0.058 798 Dihedral : 5.938 59.945 660 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.81 % Allowed : 23.57 % Favored : 72.62 % 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: 1.85 (0.34), residues: 616 helix: 1.63 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -1.98 (0.72), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.007 0.001 HIS D 300 PHE 0.031 0.002 PHE B 262 TYR 0.041 0.002 TYR A 234 ARG 0.002 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: -0.1674 (OUTLIER) cc_final: -0.3623 (mmtt) REVERT: C 257 MET cc_start: -0.2701 (mtt) cc_final: -0.3547 (mmt) REVERT: C 460 ILE cc_start: 0.2116 (pt) cc_final: 0.1798 (pt) REVERT: D 296 ILE cc_start: 0.5856 (pp) cc_final: 0.5577 (pp) outliers start: 22 outliers final: 14 residues processed: 86 average time/residue: 0.1268 time to fit residues: 15.0465 Evaluate side-chains 79 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 50 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 19 optimal weight: 40.0000 overall best weight: 8.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2945 moved from start: 1.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 5030 Z= 0.311 Angle : 0.990 12.538 6855 Z= 0.473 Chirality : 0.048 0.378 904 Planarity : 0.007 0.062 798 Dihedral : 6.016 58.882 660 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.12 % Allowed : 24.44 % Favored : 72.44 % 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: 1.77 (0.34), residues: 616 helix: 1.59 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.18 (0.70), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 453 HIS 0.007 0.002 HIS B 306 PHE 0.039 0.002 PHE B 262 TYR 0.037 0.003 TYR A 234 ARG 0.003 0.001 ARG A 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: -0.0541 (mmt) cc_final: -0.1433 (tpt) REVERT: C 257 MET cc_start: -0.2704 (mtt) cc_final: -0.3342 (mmt) REVERT: C 460 ILE cc_start: 0.2285 (pt) cc_final: 0.1947 (pt) REVERT: D 296 ILE cc_start: 0.5888 (pp) cc_final: 0.5628 (pp) REVERT: E 459 PHE cc_start: 0.3982 (t80) cc_final: 0.3405 (t80) outliers start: 18 outliers final: 12 residues processed: 78 average time/residue: 0.1307 time to fit residues: 14.1303 Evaluate side-chains 74 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 40.0000 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 50.0000 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.096948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.091574 restraints weight = 72176.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.090708 restraints weight = 93370.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.090707 restraints weight = 110357.933| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3945 moved from start: 1.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 5030 Z= 0.294 Angle : 0.997 13.315 6855 Z= 0.470 Chirality : 0.048 0.391 904 Planarity : 0.007 0.058 798 Dihedral : 5.576 56.955 658 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 23.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.91 % Allowed : 26.17 % Favored : 71.92 % 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: 1.81 (0.34), residues: 616 helix: 1.66 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -2.22 (0.65), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 453 HIS 0.006 0.001 HIS B 306 PHE 0.040 0.002 PHE B 262 TYR 0.035 0.003 TYR A 234 ARG 0.004 0.001 ARG B 282 =============================================================================== Job complete usr+sys time: 1026.80 seconds wall clock time: 19 minutes 28.68 seconds (1168.68 seconds total)