Starting phenix.real_space_refine on Fri Feb 16 13:30:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu4_21905/02_2024/6wu4_21905_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu4_21905/02_2024/6wu4_21905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu4_21905/02_2024/6wu4_21905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu4_21905/02_2024/6wu4_21905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu4_21905/02_2024/6wu4_21905_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu4_21905/02_2024/6wu4_21905_neut.pdb" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.266 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 5034 2.51 5 N 1176 2.21 5 O 1260 1.98 5 H 7812 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 458": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15332 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 7666 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain: "B" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 7666 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 22, 'TRANS': 466} Time building chain proxies: 6.84, per 1000 atoms: 0.45 Number of scatterers: 15332 At special positions: 0 Unit cell: (90.8725, 108.713, 76.935, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 O 1260 8.00 N 1176 7.00 C 5034 6.00 H 7812 1.00 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: 14.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1784 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 8 through 11 Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.510A pdb=" N LEU A 16 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 29 Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'A' and resid 57 through 72 Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 98 through 118 removed outlier: 4.161A pdb=" N TRP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'A' and resid 135 through 150 removed outlier: 4.042A pdb=" N GLY A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.649A pdb=" N THR A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.578A pdb=" N VAL A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.987A pdb=" N LYS A 185 " --> pdb=" O PRO A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 206 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 224 removed outlier: 3.777A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 255 removed outlier: 3.611A pdb=" N PHE A 233 " --> pdb=" O TRP A 229 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 280 through 300 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 335 through 359 removed outlier: 3.998A pdb=" N TRP A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 removed outlier: 3.657A pdb=" N VAL A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 392 Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 398 through 406 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.756A pdb=" N SER A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 455 through 485 Processing helix chain 'B' and resid 8 through 11 Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.511A pdb=" N LEU B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 17 " --> pdb=" O ILE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 29 Processing helix chain 'B' and resid 35 through 54 Processing helix chain 'B' and resid 57 through 72 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 98 through 118 removed outlier: 4.160A pdb=" N TRP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 132 Processing helix chain 'B' and resid 135 through 150 removed outlier: 4.040A pdb=" N GLY B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.648A pdb=" N THR B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.577A pdb=" N VAL B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.985A pdb=" N LYS B 185 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 206 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 224 removed outlier: 3.778A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 255 removed outlier: 3.612A pdb=" N PHE B 233 " --> pdb=" O TRP B 229 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B 238 " --> pdb=" O TRP B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Proline residue: B 248 - end of helix Processing helix chain 'B' and resid 264 through 277 Processing helix chain 'B' and resid 280 through 300 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 335 through 359 removed outlier: 3.998A pdb=" N TRP B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 372 removed outlier: 3.658A pdb=" N VAL B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 392 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 398 through 406 Processing helix chain 'B' and resid 406 through 415 Processing helix chain 'B' and resid 419 through 434 removed outlier: 3.757A pdb=" N SER B 423 " --> pdb=" O PRO B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 449 Processing helix chain 'B' and resid 455 through 485 530 hydrogen bonds defined for protein. 1548 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: 5.83 Time building geometry restraints manager: 15.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7808 1.03 - 1.22: 4 1.22 - 1.42: 3146 1.42 - 1.61: 4492 1.61 - 1.81: 96 Bond restraints: 15546 Sorted by residual: bond pdb=" C ALA A 75 " pdb=" N PRO A 76 " ideal model delta sigma weight residual 1.331 1.310 0.021 1.21e-02 6.83e+03 3.09e+00 bond pdb=" C ALA B 75 " pdb=" N PRO B 76 " ideal model delta sigma weight residual 1.331 1.310 0.021 1.21e-02 6.83e+03 3.09e+00 bond pdb=" CB THR A 143 " pdb=" CG2 THR A 143 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.83e+00 bond pdb=" CB THR B 143 " pdb=" CG2 THR B 143 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.68e+00 bond pdb=" CG1 ILE A 343 " pdb=" CD1 ILE A 343 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.34e+00 ... (remaining 15541 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.42: 176 105.42 - 112.57: 18615 112.57 - 119.73: 3832 119.73 - 126.89: 5495 126.89 - 134.04: 164 Bond angle restraints: 28282 Sorted by residual: angle pdb=" N GLY A 32 " pdb=" CA GLY A 32 " pdb=" C GLY A 32 " ideal model delta sigma weight residual 114.61 110.37 4.24 1.49e+00 4.50e-01 8.08e+00 angle pdb=" N GLY B 32 " pdb=" CA GLY B 32 " pdb=" C GLY B 32 " ideal model delta sigma weight residual 114.61 110.39 4.22 1.49e+00 4.50e-01 8.02e+00 angle pdb=" C ILE A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta sigma weight residual 120.28 117.04 3.24 1.34e+00 5.57e-01 5.83e+00 angle pdb=" C ILE B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 120.28 117.05 3.23 1.34e+00 5.57e-01 5.82e+00 angle pdb=" CA TRP A 344 " pdb=" CB TRP A 344 " pdb=" CG TRP A 344 " ideal model delta sigma weight residual 113.60 117.49 -3.89 1.90e+00 2.77e-01 4.18e+00 ... (remaining 28277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 6334 17.53 - 35.06: 662 35.06 - 52.59: 205 52.59 - 70.12: 60 70.12 - 87.65: 13 Dihedral angle restraints: 7274 sinusoidal: 3848 harmonic: 3426 Sorted by residual: dihedral pdb=" CA PRO B 57 " pdb=" C PRO B 57 " pdb=" N ILE B 58 " pdb=" CA ILE B 58 " ideal model delta harmonic sigma weight residual 180.00 -157.07 -22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PRO A 57 " pdb=" C PRO A 57 " pdb=" N ILE A 58 " pdb=" CA ILE A 58 " ideal model delta harmonic sigma weight residual 180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LYS A 54 " pdb=" C LYS A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta harmonic sigma weight residual 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 7271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 612 0.031 - 0.062: 375 0.062 - 0.093: 211 0.093 - 0.124: 38 0.124 - 0.154: 6 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA ILE A 375 " pdb=" N ILE A 375 " pdb=" C ILE A 375 " pdb=" CB ILE A 375 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ILE B 375 " pdb=" N ILE B 375 " pdb=" C ILE B 375 " pdb=" CB ILE B 375 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA PRO A 57 " pdb=" N PRO A 57 " pdb=" C PRO A 57 " pdb=" CB PRO A 57 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1239 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 475 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C GLY B 475 " -0.023 2.00e-02 2.50e+03 pdb=" O GLY B 475 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE B 476 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 475 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C GLY A 475 " 0.023 2.00e-02 2.50e+03 pdb=" O GLY A 475 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 476 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 143 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C THR B 143 " -0.022 2.00e-02 2.50e+03 pdb=" O THR B 143 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY B 144 " 0.007 2.00e-02 2.50e+03 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 419 2.11 - 2.74: 28614 2.74 - 3.36: 44649 3.36 - 3.98: 54541 3.98 - 4.60: 88981 Nonbonded interactions: 217204 Sorted by model distance: nonbonded pdb=" O GLY A 475 " pdb=" HG1 THR A 479 " model vdw 1.493 1.850 nonbonded pdb=" O GLY B 475 " pdb=" HG1 THR B 479 " model vdw 1.553 1.850 nonbonded pdb=" OE1 GLN A 307 " pdb=" H GLN A 307 " model vdw 1.567 1.850 nonbonded pdb=" OE1 GLN B 307 " pdb=" H GLN B 307 " model vdw 1.569 1.850 nonbonded pdb=" O THR B 438 " pdb=" HE1 TRP B 459 " model vdw 1.587 1.850 ... (remaining 217199 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 'B' } 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: 2.320 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: 0.230 Extract box with map and model: 12.070 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 54.840 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.010 0.078 7734 Z= 0.647 Angle : 0.679 6.653 10550 Z= 0.372 Chirality : 0.047 0.154 1242 Planarity : 0.004 0.032 1254 Dihedral : 13.822 78.532 2650 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.73 % Favored : 86.86 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: -4.78 (0.20), residues: 974 helix: -2.48 (0.15), residues: 726 sheet: None (None), residues: 0 loop : -4.82 (0.24), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.005 0.002 HIS A 401 PHE 0.015 0.002 PHE B 367 TYR 0.012 0.002 TYR B 255 ARG 0.002 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.8662 (t0) cc_final: 0.8248 (t0) REVERT: A 176 ASP cc_start: 0.8191 (t70) cc_final: 0.7442 (t0) REVERT: A 286 MET cc_start: 0.7473 (tpt) cc_final: 0.7122 (tpt) REVERT: A 335 GLU cc_start: 0.8229 (tp30) cc_final: 0.7701 (tp30) REVERT: A 369 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 436 SER cc_start: 0.9276 (p) cc_final: 0.9035 (p) REVERT: B 8 ASN cc_start: 0.8636 (t0) cc_final: 0.8261 (t0) REVERT: B 10 LYS cc_start: 0.9138 (mtmt) cc_final: 0.8884 (mttm) REVERT: B 176 ASP cc_start: 0.8229 (t70) cc_final: 0.7481 (t0) REVERT: B 286 MET cc_start: 0.7481 (tpt) cc_final: 0.7138 (tpt) REVERT: B 335 GLU cc_start: 0.8180 (tp30) cc_final: 0.7693 (tp30) REVERT: B 369 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8659 (tm-30) REVERT: B 436 SER cc_start: 0.9290 (p) cc_final: 0.9058 (p) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.3525 time to fit residues: 74.3281 Evaluate side-chains 128 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7734 Z= 0.191 Angle : 0.566 4.992 10550 Z= 0.297 Chirality : 0.040 0.162 1242 Planarity : 0.004 0.034 1254 Dihedral : 4.599 21.030 1016 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.88 % Favored : 92.92 % Rotamer: Outliers : 0.25 % Allowed : 10.76 % Favored : 88.99 % 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: -2.42 (0.25), residues: 974 helix: -0.70 (0.18), residues: 750 sheet: None (None), residues: 0 loop : -4.52 (0.27), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 344 HIS 0.007 0.002 HIS B 197 PHE 0.008 0.001 PHE B 193 TYR 0.009 0.001 TYR B 190 ARG 0.002 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.8659 (t0) cc_final: 0.8210 (t0) REVERT: A 10 LYS cc_start: 0.9231 (mtmt) cc_final: 0.8942 (mttm) REVERT: A 176 ASP cc_start: 0.8291 (t70) cc_final: 0.7580 (t0) REVERT: A 335 GLU cc_start: 0.8219 (tp30) cc_final: 0.7579 (tp30) REVERT: A 369 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8787 (tm-30) REVERT: B 8 ASN cc_start: 0.8642 (t0) cc_final: 0.8235 (t0) REVERT: B 10 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8966 (mttm) REVERT: B 176 ASP cc_start: 0.8327 (t70) cc_final: 0.7615 (t0) REVERT: B 286 MET cc_start: 0.7643 (tpt) cc_final: 0.7273 (tpt) REVERT: B 335 GLU cc_start: 0.8158 (tp30) cc_final: 0.7576 (tp30) REVERT: B 369 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8817 (tm-30) outliers start: 2 outliers final: 2 residues processed: 134 average time/residue: 0.3207 time to fit residues: 64.0046 Evaluate side-chains 124 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7734 Z= 0.351 Angle : 0.623 5.018 10550 Z= 0.331 Chirality : 0.042 0.166 1242 Planarity : 0.004 0.032 1254 Dihedral : 4.594 22.150 1016 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.11 % Favored : 91.68 % Rotamer: Outliers : 1.01 % Allowed : 13.67 % Favored : 85.32 % 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: -1.26 (0.26), residues: 974 helix: 0.21 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -4.19 (0.28), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 102 HIS 0.008 0.002 HIS B 197 PHE 0.012 0.001 PHE B 364 TYR 0.016 0.002 TYR B 255 ARG 0.001 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9323 (mtmt) cc_final: 0.8929 (mttm) REVERT: A 98 ASN cc_start: 0.8579 (t0) cc_final: 0.8286 (m-40) REVERT: A 176 ASP cc_start: 0.8462 (t70) cc_final: 0.7892 (t0) REVERT: A 233 PHE cc_start: 0.8788 (t80) cc_final: 0.8377 (t80) REVERT: A 253 LYS cc_start: 0.8388 (tmtt) cc_final: 0.8093 (tttp) REVERT: A 303 PHE cc_start: 0.8045 (m-80) cc_final: 0.7618 (m-10) REVERT: A 434 ASN cc_start: 0.8538 (m110) cc_final: 0.8329 (m110) REVERT: B 8 ASN cc_start: 0.8798 (t0) cc_final: 0.8326 (t0) REVERT: B 10 LYS cc_start: 0.9335 (mtmt) cc_final: 0.9038 (mttm) REVERT: B 176 ASP cc_start: 0.8493 (t70) cc_final: 0.7927 (t0) REVERT: B 233 PHE cc_start: 0.8781 (t80) cc_final: 0.8450 (t80) REVERT: B 253 LYS cc_start: 0.8393 (tmtt) cc_final: 0.7984 (tttp) REVERT: B 286 MET cc_start: 0.7827 (tpt) cc_final: 0.7407 (tpt) REVERT: B 303 PHE cc_start: 0.8095 (m-80) cc_final: 0.7673 (m-10) outliers start: 8 outliers final: 7 residues processed: 191 average time/residue: 0.3201 time to fit residues: 90.0265 Evaluate side-chains 188 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 181 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 305 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7734 Z= 0.223 Angle : 0.558 5.042 10550 Z= 0.292 Chirality : 0.040 0.163 1242 Planarity : 0.004 0.037 1254 Dihedral : 4.493 21.745 1016 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.85 % Favored : 93.94 % Rotamer: Outliers : 0.76 % Allowed : 18.73 % Favored : 80.51 % 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: -0.48 (0.27), residues: 974 helix: 0.68 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -3.63 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.005 0.001 HIS A 197 PHE 0.007 0.001 PHE A 96 TYR 0.018 0.001 TYR A 252 ARG 0.001 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9345 (mtmt) cc_final: 0.8950 (mttm) REVERT: A 174 SER cc_start: 0.9096 (t) cc_final: 0.8687 (p) REVERT: A 176 ASP cc_start: 0.8445 (t70) cc_final: 0.7938 (t0) REVERT: A 233 PHE cc_start: 0.8776 (t80) cc_final: 0.8443 (t80) REVERT: A 253 LYS cc_start: 0.8306 (tmtt) cc_final: 0.7853 (tttp) REVERT: A 303 PHE cc_start: 0.8066 (m-80) cc_final: 0.7633 (m-10) REVERT: A 335 GLU cc_start: 0.8720 (tp30) cc_final: 0.7949 (tp30) REVERT: B 8 ASN cc_start: 0.8789 (t0) cc_final: 0.8296 (t0) REVERT: B 10 LYS cc_start: 0.9351 (mtmt) cc_final: 0.9049 (mttm) REVERT: B 174 SER cc_start: 0.9090 (t) cc_final: 0.8680 (p) REVERT: B 176 ASP cc_start: 0.8454 (t70) cc_final: 0.7940 (t0) REVERT: B 303 PHE cc_start: 0.8098 (m-80) cc_final: 0.7730 (m-10) REVERT: B 335 GLU cc_start: 0.8703 (tp30) cc_final: 0.7958 (tp30) outliers start: 6 outliers final: 5 residues processed: 187 average time/residue: 0.3549 time to fit residues: 99.4817 Evaluate side-chains 182 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 485 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7734 Z= 0.218 Angle : 0.545 4.890 10550 Z= 0.284 Chirality : 0.039 0.162 1242 Planarity : 0.004 0.037 1254 Dihedral : 4.443 22.470 1016 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.57 % Favored : 93.22 % Rotamer: Outliers : 1.52 % Allowed : 18.73 % Favored : 79.75 % 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: 0.04 (0.27), residues: 974 helix: 0.98 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -3.24 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 344 HIS 0.005 0.001 HIS B 197 PHE 0.008 0.001 PHE A 96 TYR 0.013 0.001 TYR A 252 ARG 0.001 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9367 (mtmt) cc_final: 0.8968 (mttm) REVERT: A 174 SER cc_start: 0.9110 (t) cc_final: 0.8675 (p) REVERT: A 176 ASP cc_start: 0.8449 (t70) cc_final: 0.7973 (t0) REVERT: A 303 PHE cc_start: 0.8115 (m-80) cc_final: 0.7751 (m-10) REVERT: A 335 GLU cc_start: 0.8674 (tp30) cc_final: 0.7886 (tp30) REVERT: B 10 LYS cc_start: 0.9366 (mtmt) cc_final: 0.9002 (mttm) REVERT: B 174 SER cc_start: 0.9106 (t) cc_final: 0.8680 (p) REVERT: B 176 ASP cc_start: 0.8469 (t70) cc_final: 0.7989 (t0) REVERT: B 303 PHE cc_start: 0.8141 (m-80) cc_final: 0.7776 (m-10) REVERT: B 335 GLU cc_start: 0.8663 (tp30) cc_final: 0.7888 (tp30) outliers start: 12 outliers final: 8 residues processed: 188 average time/residue: 0.3169 time to fit residues: 88.3636 Evaluate side-chains 190 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 485 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7734 Z= 0.275 Angle : 0.569 5.573 10550 Z= 0.300 Chirality : 0.040 0.162 1242 Planarity : 0.004 0.037 1254 Dihedral : 4.485 22.433 1016 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.47 % Favored : 93.33 % Rotamer: Outliers : 1.39 % Allowed : 19.11 % Favored : 79.49 % 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: 0.24 (0.27), residues: 974 helix: 1.12 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -3.12 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 344 HIS 0.006 0.001 HIS B 197 PHE 0.008 0.001 PHE A 96 TYR 0.012 0.001 TYR A 252 ARG 0.001 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9381 (mtmt) cc_final: 0.8983 (mttm) REVERT: A 176 ASP cc_start: 0.8512 (t70) cc_final: 0.8081 (t70) REVERT: A 303 PHE cc_start: 0.8198 (m-80) cc_final: 0.7839 (m-10) REVERT: A 335 GLU cc_start: 0.8717 (tp30) cc_final: 0.7849 (tp30) REVERT: A 416 MET cc_start: 0.8504 (mmm) cc_final: 0.8174 (mmt) REVERT: B 10 LYS cc_start: 0.9381 (mtmt) cc_final: 0.9009 (mttm) REVERT: B 176 ASP cc_start: 0.8525 (t70) cc_final: 0.8092 (t70) REVERT: B 303 PHE cc_start: 0.8230 (m-80) cc_final: 0.7870 (m-10) REVERT: B 335 GLU cc_start: 0.8724 (tp30) cc_final: 0.7860 (tp30) outliers start: 11 outliers final: 10 residues processed: 198 average time/residue: 0.3310 time to fit residues: 95.3817 Evaluate side-chains 199 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 189 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TRP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 485 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7734 Z= 0.182 Angle : 0.530 4.954 10550 Z= 0.274 Chirality : 0.039 0.161 1242 Planarity : 0.004 0.039 1254 Dihedral : 4.402 22.714 1016 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.16 % Favored : 93.63 % Rotamer: Outliers : 1.90 % Allowed : 19.24 % Favored : 78.86 % 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: 0.64 (0.28), residues: 974 helix: 1.38 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -2.88 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.005 0.001 HIS B 197 PHE 0.007 0.001 PHE A 96 TYR 0.010 0.001 TYR A 252 ARG 0.001 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9381 (mtmt) cc_final: 0.8983 (mttm) REVERT: A 176 ASP cc_start: 0.8450 (t70) cc_final: 0.8033 (t0) REVERT: A 303 PHE cc_start: 0.8169 (m-80) cc_final: 0.7798 (m-10) REVERT: A 335 GLU cc_start: 0.8597 (tp30) cc_final: 0.7700 (tp30) REVERT: A 416 MET cc_start: 0.8523 (mmm) cc_final: 0.8182 (mmt) REVERT: A 425 MET cc_start: 0.8614 (tpp) cc_final: 0.8410 (tpp) REVERT: B 10 LYS cc_start: 0.9381 (mtmt) cc_final: 0.9007 (mttm) REVERT: B 176 ASP cc_start: 0.8466 (t70) cc_final: 0.8032 (t0) REVERT: B 303 PHE cc_start: 0.8199 (m-80) cc_final: 0.7868 (m-10) REVERT: B 335 GLU cc_start: 0.8592 (tp30) cc_final: 0.7710 (tp30) REVERT: B 388 MET cc_start: 0.7927 (ttt) cc_final: 0.7711 (ttt) outliers start: 15 outliers final: 9 residues processed: 194 average time/residue: 0.3263 time to fit residues: 92.9058 Evaluate side-chains 195 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TRP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 485 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7734 Z= 0.179 Angle : 0.528 4.784 10550 Z= 0.273 Chirality : 0.039 0.160 1242 Planarity : 0.004 0.040 1254 Dihedral : 4.360 22.580 1016 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 1.52 % Allowed : 20.13 % Favored : 78.35 % 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: 0.90 (0.28), residues: 974 helix: 1.54 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -2.72 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.005 0.001 HIS B 197 PHE 0.007 0.001 PHE A 96 TYR 0.012 0.001 TYR A 252 ARG 0.001 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9384 (mtmt) cc_final: 0.8982 (mttm) REVERT: A 106 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8663 (mmp) REVERT: A 176 ASP cc_start: 0.8469 (t70) cc_final: 0.8058 (t0) REVERT: A 303 PHE cc_start: 0.8189 (m-80) cc_final: 0.7850 (m-10) REVERT: A 335 GLU cc_start: 0.8549 (tp30) cc_final: 0.7667 (tp30) REVERT: A 416 MET cc_start: 0.8540 (mmm) cc_final: 0.8187 (mmt) REVERT: B 10 LYS cc_start: 0.9387 (mtmt) cc_final: 0.9005 (mttm) REVERT: B 106 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8657 (mmp) REVERT: B 176 ASP cc_start: 0.8473 (t70) cc_final: 0.8048 (t0) REVERT: B 303 PHE cc_start: 0.8202 (m-80) cc_final: 0.7871 (m-10) REVERT: B 335 GLU cc_start: 0.8558 (tp30) cc_final: 0.7683 (tp30) REVERT: B 388 MET cc_start: 0.7937 (ttt) cc_final: 0.7715 (ttt) REVERT: B 425 MET cc_start: 0.8563 (tpp) cc_final: 0.8355 (tpp) outliers start: 12 outliers final: 8 residues processed: 189 average time/residue: 0.3660 time to fit residues: 102.5215 Evaluate side-chains 194 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TRP Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 485 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7734 Z= 0.279 Angle : 0.563 4.729 10550 Z= 0.297 Chirality : 0.040 0.162 1242 Planarity : 0.004 0.038 1254 Dihedral : 4.426 22.607 1016 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.57 % Favored : 93.22 % Rotamer: Outliers : 1.65 % Allowed : 20.13 % Favored : 78.23 % 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: 0.82 (0.28), residues: 974 helix: 1.48 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -2.71 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.006 0.001 HIS B 197 PHE 0.008 0.001 PHE B 96 TYR 0.013 0.001 TYR A 252 ARG 0.001 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9388 (mtmt) cc_final: 0.8986 (mttm) REVERT: A 106 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8649 (mmp) REVERT: A 176 ASP cc_start: 0.8484 (t70) cc_final: 0.8070 (t70) REVERT: A 255 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8439 (t80) REVERT: A 258 GLU cc_start: 0.8778 (tt0) cc_final: 0.8556 (mt-10) REVERT: A 303 PHE cc_start: 0.8271 (m-80) cc_final: 0.7921 (m-10) REVERT: A 335 GLU cc_start: 0.8661 (tp30) cc_final: 0.7737 (tp30) REVERT: A 416 MET cc_start: 0.8522 (mmm) cc_final: 0.8168 (mmt) REVERT: B 10 LYS cc_start: 0.9396 (mtmt) cc_final: 0.9015 (mttm) REVERT: B 106 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8627 (mmp) REVERT: B 176 ASP cc_start: 0.8494 (t70) cc_final: 0.8071 (t70) REVERT: B 255 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8363 (t80) REVERT: B 258 GLU cc_start: 0.8761 (tt0) cc_final: 0.8455 (mt-10) REVERT: B 303 PHE cc_start: 0.8282 (m-80) cc_final: 0.7932 (m-10) REVERT: B 335 GLU cc_start: 0.8681 (tp30) cc_final: 0.7770 (tp30) REVERT: B 388 MET cc_start: 0.8017 (ttt) cc_final: 0.7776 (ttt) outliers start: 13 outliers final: 9 residues processed: 197 average time/residue: 0.3130 time to fit residues: 90.3404 Evaluate side-chains 203 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TRP Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 485 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7734 Z= 0.166 Angle : 0.524 4.752 10550 Z= 0.270 Chirality : 0.039 0.159 1242 Planarity : 0.004 0.039 1254 Dihedral : 4.371 22.635 1016 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.75 % Favored : 94.05 % Rotamer: Outliers : 1.27 % Allowed : 20.51 % Favored : 78.23 % 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: 1.11 (0.28), residues: 974 helix: 1.66 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -2.48 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.005 0.001 HIS B 197 PHE 0.006 0.001 PHE B 96 TYR 0.012 0.001 TYR A 252 ARG 0.001 0.000 ARG A 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9388 (mtmt) cc_final: 0.8988 (mttm) REVERT: A 106 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8612 (mmp) REVERT: A 176 ASP cc_start: 0.8423 (t70) cc_final: 0.8034 (t70) REVERT: A 255 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8274 (t80) REVERT: A 258 GLU cc_start: 0.8762 (tt0) cc_final: 0.8506 (mt-10) REVERT: A 283 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8667 (mm-30) REVERT: A 303 PHE cc_start: 0.8201 (m-80) cc_final: 0.7883 (m-10) REVERT: A 335 GLU cc_start: 0.8541 (tp30) cc_final: 0.7651 (tp30) REVERT: A 416 MET cc_start: 0.8552 (mmm) cc_final: 0.8171 (mmt) REVERT: B 10 LYS cc_start: 0.9394 (mtmt) cc_final: 0.9013 (mttm) REVERT: B 106 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8559 (mmp) REVERT: B 176 ASP cc_start: 0.8441 (t70) cc_final: 0.8051 (t70) REVERT: B 258 GLU cc_start: 0.8737 (tt0) cc_final: 0.8408 (mt-10) REVERT: B 303 PHE cc_start: 0.8232 (m-80) cc_final: 0.7913 (m-10) REVERT: B 335 GLU cc_start: 0.8552 (tp30) cc_final: 0.7681 (tp30) REVERT: B 388 MET cc_start: 0.7970 (ttt) cc_final: 0.7734 (ttt) REVERT: B 416 MET cc_start: 0.8497 (mmm) cc_final: 0.8162 (mmt) outliers start: 10 outliers final: 7 residues processed: 191 average time/residue: 0.3292 time to fit residues: 92.5826 Evaluate side-chains 197 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TRP Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 485 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 76 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** 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 = 0.3102 r_free = 0.3102 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.088111 restraints weight = 32341.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.092679 restraints weight = 12054.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.095759 restraints weight = 6696.001| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7734 Z= 0.156 Angle : 0.519 4.704 10550 Z= 0.266 Chirality : 0.039 0.154 1242 Planarity : 0.004 0.041 1254 Dihedral : 4.323 23.172 1016 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 1.14 % Allowed : 20.63 % Favored : 78.23 % 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: 1.45 (0.28), residues: 974 helix: 1.87 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.005 0.001 HIS B 197 PHE 0.006 0.001 PHE B 389 TYR 0.018 0.001 TYR B 252 ARG 0.001 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3681.36 seconds wall clock time: 66 minutes 10.13 seconds (3970.13 seconds total)