Starting phenix.real_space_refine on Thu Dec 7 21:33:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/12_2023/1oed_1044.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/12_2023/1oed_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_1044/12_2023/1oed_1044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/12_2023/1oed_1044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/12_2023/1oed_1044.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/12_2023/1oed_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-1.21rc1-5172/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: 3.13, per 1000 atoms: 0.64 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: 2.14 Conformation dependent library (CDL) restraints added in 852.2 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: 0.37 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: 1.40 Time building geometry restraints manager: 2.30 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: 0.050 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 17.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- 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 : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 46 residues processed: 198 average time/residue: 0.1487 time to fit residues: 38.0235 Evaluate side-chains 118 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 72 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.0817 time to fit residues: 6.2878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 30.0000 chunk 25 optimal weight: 50.0000 chunk 15 optimal weight: 40.0000 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 50.0000 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN ** 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 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: 0.2052 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 5030 Z= 0.441 Angle : 1.151 11.449 6855 Z= 0.587 Chirality : 0.056 0.442 904 Planarity : 0.009 0.066 798 Dihedral : 5.955 24.251 654 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 39.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.03 % Allowed : 20.10 % Favored : 74.87 % 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: -1.72 (0.32), residues: 616 helix: -0.79 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -2.80 (0.75), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 453 HIS 0.007 0.002 HIS D 300 PHE 0.038 0.003 PHE C 314 TYR 0.032 0.003 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 107 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 78 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 7 residues processed: 98 average time/residue: 0.1364 time to fit residues: 18.0272 Evaluate side-chains 65 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0480 time to fit residues: 1.3548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2235 moved from start: 0.8687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5030 Z= 0.338 Angle : 0.965 12.368 6855 Z= 0.483 Chirality : 0.050 0.328 904 Planarity : 0.007 0.068 798 Dihedral : 5.895 25.371 654 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 29.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.47 % Allowed : 21.32 % Favored : 75.22 % 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: -0.96 (0.32), residues: 616 helix: -0.27 (0.21), residues: 551 sheet: None (None), residues: 0 loop : -2.64 (0.66), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 453 HIS 0.005 0.001 HIS B 306 PHE 0.039 0.003 PHE D 256 TYR 0.010 0.001 TYR B 220 ARG 0.005 0.001 ARG B 282 *********************** 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 91 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 85 average time/residue: 0.1442 time to fit residues: 16.5612 Evaluate side-chains 59 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0546 time to fit residues: 1.1641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 40.0000 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 40.0000 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- 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** B 466 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2419 moved from start: 1.0119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5030 Z= 0.336 Angle : 0.955 10.373 6855 Z= 0.462 Chirality : 0.048 0.228 904 Planarity : 0.007 0.068 798 Dihedral : 5.465 25.476 654 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 26.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.12 % Allowed : 21.32 % 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: -0.16 (0.32), residues: 616 helix: 0.22 (0.21), residues: 552 sheet: None (None), residues: 0 loop : -1.90 (0.68), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 453 HIS 0.005 0.001 HIS B 460 PHE 0.033 0.002 PHE D 256 TYR 0.015 0.002 TYR B 220 ARG 0.005 0.001 ARG C 277 *********************** 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 79 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 75 average time/residue: 0.1440 time to fit residues: 14.5213 Evaluate side-chains 62 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0467 time to fit residues: 1.3875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2609 moved from start: 1.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5030 Z= 0.322 Angle : 0.920 12.733 6855 Z= 0.450 Chirality : 0.045 0.216 904 Planarity : 0.008 0.066 798 Dihedral : 5.412 23.834 654 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.77 % Allowed : 22.01 % Favored : 75.22 % 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: 0.70 (0.33), residues: 616 helix: 0.88 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -2.32 (0.62), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 453 HIS 0.008 0.002 HIS D 300 PHE 0.031 0.002 PHE D 256 TYR 0.017 0.002 TYR B 220 ARG 0.004 0.001 ARG C 277 *********************** 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 83 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 79 average time/residue: 0.1450 time to fit residues: 15.4495 Evaluate side-chains 67 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0575 time to fit residues: 1.4681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 50.0000 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 42 optimal weight: 0.0470 overall best weight: 3.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** 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: 0.2583 moved from start: 1.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5030 Z= 0.272 Angle : 0.877 12.409 6855 Z= 0.419 Chirality : 0.045 0.427 904 Planarity : 0.007 0.061 798 Dihedral : 5.176 23.209 654 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.21 % Allowed : 23.92 % Favored : 74.87 % 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: 1.17 (0.34), residues: 616 helix: 1.17 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.07 (0.68), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.015 0.002 HIS B 306 PHE 0.028 0.002 PHE D 256 TYR 0.008 0.001 TYR B 220 ARG 0.001 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 73 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 0.1505 time to fit residues: 14.4536 Evaluate side-chains 64 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0440 time to fit residues: 0.9106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2602 moved from start: 1.2555 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= 0.263 Angle : 0.848 12.481 6855 Z= 0.408 Chirality : 0.043 0.184 904 Planarity : 0.007 0.058 798 Dihedral : 4.944 22.190 654 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.87 % Allowed : 24.44 % 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: 1.48 (0.34), residues: 616 helix: 1.37 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.02 (0.69), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 453 HIS 0.009 0.001 HIS D 300 PHE 0.026 0.002 PHE C 314 TYR 0.016 0.001 TYR A 213 ARG 0.005 0.000 ARG C 277 *********************** 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 72 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.1304 time to fit residues: 12.7612 Evaluate side-chains 65 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0688 time to fit residues: 0.8309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 50 optimal weight: 40.0000 chunk 53 optimal weight: 40.0000 chunk 32 optimal weight: 30.0000 chunk 23 optimal weight: 40.0000 chunk 42 optimal weight: 0.0370 chunk 16 optimal weight: 30.0000 overall best weight: 8.2068 ------------------------------------------------------------------------------- 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** ** 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: 0.2758 moved from start: 1.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5030 Z= 0.287 Angle : 0.926 11.459 6855 Z= 0.443 Chirality : 0.046 0.401 904 Planarity : 0.007 0.059 798 Dihedral : 4.973 21.597 654 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.87 % Allowed : 24.44 % 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: 1.47 (0.34), residues: 616 helix: 1.41 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -2.33 (0.65), residues: 69 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 0.025 0.002 PHE B 262 TYR 0.015 0.002 TYR B 220 ARG 0.003 0.000 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 71 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 69 average time/residue: 0.1200 time to fit residues: 11.7442 Evaluate side-chains 66 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0478 time to fit residues: 0.9267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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** ** 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: 0.2885 moved from start: 1.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5030 Z= 0.295 Angle : 0.935 12.545 6855 Z= 0.447 Chirality : 0.048 0.399 904 Planarity : 0.007 0.058 798 Dihedral : 5.056 20.344 654 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.56 % Allowed : 24.09 % 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: 1.68 (0.34), residues: 616 helix: 1.54 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -2.17 (0.70), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.008 0.002 HIS D 300 PHE 0.033 0.002 PHE B 262 TYR 0.044 0.003 TYR A 234 ARG 0.002 0.000 ARG D 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 81 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 78 average time/residue: 0.1419 time to fit residues: 14.8610 Evaluate side-chains 63 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0593 time to fit residues: 0.9524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 37 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2989 moved from start: 1.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5030 Z= 0.314 Angle : 0.998 14.565 6855 Z= 0.472 Chirality : 0.049 0.409 904 Planarity : 0.007 0.056 798 Dihedral : 5.073 20.388 654 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.17 % Allowed : 25.65 % Favored : 74.18 % 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: 1.55 (0.34), residues: 616 helix: 1.45 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -2.15 (0.72), 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 0.036 0.002 PHE E 459 TYR 0.016 0.002 TYR B 283 ARG 0.004 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 64 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.1377 time to fit residues: 12.3769 Evaluate side-chains 60 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 0.0010 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 1 optimal weight: 40.0000 chunk 38 optimal weight: 7.9990 overall best weight: 2.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS ** C 276 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** D 435 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.111785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.092614 restraints weight = 42089.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.092614 restraints weight = 53367.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.092614 restraints weight = 53367.000| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4570 moved from start: 1.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5030 Z= 0.287 Angle : 0.998 14.078 6855 Z= 0.470 Chirality : 0.048 0.353 904 Planarity : 0.007 0.058 798 Dihedral : 4.997 19.111 654 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.87 % Allowed : 26.34 % Favored : 72.79 % 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: 1.69 (0.34), residues: 616 helix: 1.55 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.33 (0.71), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 453 HIS 0.009 0.002 HIS D 300 PHE 0.040 0.002 PHE B 262 TYR 0.013 0.001 TYR B 240 ARG 0.006 0.001 ARG A 301 =============================================================================== Job complete usr+sys time: 1040.09 seconds wall clock time: 19 minutes 54.49 seconds (1194.49 seconds total)