Starting phenix.real_space_refine on Mon Apr 8 09:08:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nh9_12321/04_2024/7nh9_12321.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nh9_12321/04_2024/7nh9_12321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nh9_12321/04_2024/7nh9_12321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nh9_12321/04_2024/7nh9_12321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nh9_12321/04_2024/7nh9_12321.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nh9_12321/04_2024/7nh9_12321.pdb" } resolution = 3.03 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= 0.001 sd= 0.009 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 30 5.16 5 C 8320 2.51 5 N 2375 2.21 5 O 2395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 170": "OD1" <-> "OD2" Residue "E TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13120 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2624 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "B" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2624 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "C" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2624 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2624 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "E" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2624 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Time building chain proxies: 7.21, per 1000 atoms: 0.55 Number of scatterers: 13120 At special positions: 0 Unit cell: (122.672, 122.016, 126.608, 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 30 16.00 O 2395 8.00 N 2375 7.00 C 8320 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: 5.35 Conformation dependent library (CDL) restraints added in 2.5 seconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 56.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.536A pdb=" N GLN A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 182 removed outlier: 3.701A pdb=" N THR A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 219 removed outlier: 3.931A pdb=" N TYR A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Proline residue: A 208 - end of helix removed outlier: 3.876A pdb=" N ASP A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 228 through 289 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 313 through 331 removed outlier: 3.650A pdb=" N GLY A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 3.536A pdb=" N GLN B 55 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 182 removed outlier: 3.701A pdb=" N THR B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 219 removed outlier: 3.932A pdb=" N TYR B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Proline residue: B 208 - end of helix removed outlier: 3.876A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 228 through 289 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 313 through 331 removed outlier: 3.650A pdb=" N GLY B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.536A pdb=" N GLN C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 182 removed outlier: 3.701A pdb=" N THR C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 219 removed outlier: 3.931A pdb=" N TYR C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Proline residue: C 208 - end of helix removed outlier: 3.876A pdb=" N ASP C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 228 through 289 Proline residue: C 284 - end of helix Processing helix chain 'C' and resid 313 through 331 removed outlier: 3.651A pdb=" N GLY C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 60 removed outlier: 3.535A pdb=" N GLN D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 73 Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 182 removed outlier: 3.701A pdb=" N THR D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 219 removed outlier: 3.931A pdb=" N TYR D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Proline residue: D 208 - end of helix removed outlier: 3.876A pdb=" N ASP D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 228 through 289 Proline residue: D 284 - end of helix Processing helix chain 'D' and resid 313 through 331 removed outlier: 3.651A pdb=" N GLY D 317 " --> pdb=" O LEU D 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.536A pdb=" N GLN E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 73 Processing helix chain 'E' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 182 removed outlier: 3.700A pdb=" N THR E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 219 removed outlier: 3.931A pdb=" N TYR E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) Proline residue: E 208 - end of helix removed outlier: 3.875A pdb=" N ASP E 211 " --> pdb=" O ALA E 207 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 228 through 289 Proline residue: E 284 - end of helix Processing helix chain 'E' and resid 313 through 331 removed outlier: 3.651A pdb=" N GLY E 317 " --> pdb=" O LEU E 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.559A pdb=" N HIS A 46 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A 15 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TRP A 44 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.559A pdb=" N HIS B 46 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY B 15 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TRP B 44 " --> pdb=" O GLY B 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.560A pdb=" N HIS C 46 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY C 15 " --> pdb=" O TRP C 44 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP C 44 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.559A pdb=" N HIS D 46 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY D 15 " --> pdb=" O TRP D 44 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP D 44 " --> pdb=" O GLY D 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.559A pdb=" N HIS E 46 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY E 15 " --> pdb=" O TRP E 44 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP E 44 " --> pdb=" O GLY E 15 " (cutoff:3.500A) 795 hydrogen bonds defined for protein. 2340 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: 3.49 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4510 1.34 - 1.46: 2651 1.46 - 1.58: 6174 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 13385 Sorted by residual: bond pdb=" C THR A 77 " pdb=" N ARG A 78 " ideal model delta sigma weight residual 1.331 1.281 0.050 1.59e-02 3.96e+03 9.82e+00 bond pdb=" C THR C 77 " pdb=" N ARG C 78 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.59e-02 3.96e+03 9.65e+00 bond pdb=" C THR B 77 " pdb=" N ARG B 78 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.59e-02 3.96e+03 9.64e+00 bond pdb=" C THR E 77 " pdb=" N ARG E 78 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.59e-02 3.96e+03 9.58e+00 bond pdb=" C THR D 77 " pdb=" N ARG D 78 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.59e-02 3.96e+03 9.55e+00 ... (remaining 13380 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.54: 315 106.54 - 113.44: 7230 113.44 - 120.33: 5391 120.33 - 127.23: 5034 127.23 - 134.12: 180 Bond angle restraints: 18150 Sorted by residual: angle pdb=" C ARG E 218 " pdb=" N TYR E 219 " pdb=" CA TYR E 219 " ideal model delta sigma weight residual 121.90 116.20 5.70 1.26e+00 6.30e-01 2.05e+01 angle pdb=" C ARG A 218 " pdb=" N TYR A 219 " pdb=" CA TYR A 219 " ideal model delta sigma weight residual 121.90 116.21 5.69 1.26e+00 6.30e-01 2.04e+01 angle pdb=" C ARG D 218 " pdb=" N TYR D 219 " pdb=" CA TYR D 219 " ideal model delta sigma weight residual 121.90 116.22 5.68 1.26e+00 6.30e-01 2.03e+01 angle pdb=" C ARG C 218 " pdb=" N TYR C 219 " pdb=" CA TYR C 219 " ideal model delta sigma weight residual 121.90 116.22 5.68 1.26e+00 6.30e-01 2.03e+01 angle pdb=" C ARG B 218 " pdb=" N TYR B 219 " pdb=" CA TYR B 219 " ideal model delta sigma weight residual 121.90 116.24 5.66 1.26e+00 6.30e-01 2.02e+01 ... (remaining 18145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7160 17.92 - 35.84: 640 35.84 - 53.77: 165 53.77 - 71.69: 10 71.69 - 89.61: 15 Dihedral angle restraints: 7990 sinusoidal: 3310 harmonic: 4680 Sorted by residual: dihedral pdb=" CA LEU C 84 " pdb=" C LEU C 84 " pdb=" N GLY C 85 " pdb=" CA GLY C 85 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LEU E 84 " pdb=" C LEU E 84 " pdb=" N GLY E 85 " pdb=" CA GLY E 85 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LEU B 84 " pdb=" C LEU B 84 " pdb=" N GLY B 85 " pdb=" CA GLY B 85 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 7987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1029 0.027 - 0.054: 577 0.054 - 0.081: 208 0.081 - 0.108: 136 0.108 - 0.135: 40 Chirality restraints: 1990 Sorted by residual: chirality pdb=" CA PRO B 39 " pdb=" N PRO B 39 " pdb=" C PRO B 39 " pdb=" CB PRO B 39 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" C PRO A 39 " pdb=" CB PRO A 39 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA PRO E 39 " pdb=" N PRO E 39 " pdb=" C PRO E 39 " pdb=" CB PRO E 39 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1987 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 207 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO E 208 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 208 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 208 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 207 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 208 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 207 " -0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 208 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " -0.029 5.00e-02 4.00e+02 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2722 2.77 - 3.30: 13245 3.30 - 3.83: 22022 3.83 - 4.37: 25326 4.37 - 4.90: 43650 Nonbonded interactions: 106965 Sorted by model distance: nonbonded pdb=" OE2 GLU A 244 " pdb=" NH1 ARG E 78 " model vdw 2.236 2.520 nonbonded pdb=" OD1 ASN C 97 " pdb=" ND2 ASN C 99 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASN B 97 " pdb=" ND2 ASN B 99 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASN A 97 " pdb=" ND2 ASN A 99 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASN E 97 " pdb=" ND2 ASN E 99 " model vdw 2.249 2.520 ... (remaining 106960 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.020 Extract box with map and model: 10.830 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 36.050 Find NCS groups from input model: 0.810 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.007 0.061 13385 Z= 0.448 Angle : 0.798 7.570 18150 Z= 0.455 Chirality : 0.043 0.135 1990 Planarity : 0.004 0.051 2370 Dihedral : 14.804 89.611 4990 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 3.31 % Allowed : 8.16 % Favored : 88.53 % 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: -2.35 (0.19), residues: 1625 helix: -0.51 (0.16), residues: 920 sheet: -1.87 (0.32), residues: 230 loop : -3.31 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 57 HIS 0.003 0.001 HIS C 190 PHE 0.009 0.001 PHE A 92 TYR 0.012 0.001 TYR D 151 ARG 0.005 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 1.670 Fit side-chains REVERT: A 270 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7889 (ttp-110) REVERT: B 270 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7952 (ttp-110) REVERT: C 266 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7702 (pp20) REVERT: C 270 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7943 (ttp-110) REVERT: C 285 MET cc_start: 0.8524 (tpt) cc_final: 0.8205 (tpp) REVERT: C 322 GLN cc_start: 0.7832 (mt0) cc_final: 0.7403 (mt0) REVERT: D 128 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8296 (mmmt) REVERT: D 233 ASN cc_start: 0.9178 (t0) cc_final: 0.8961 (t0) REVERT: D 285 MET cc_start: 0.8453 (tpt) cc_final: 0.8243 (tpp) REVERT: E 270 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7894 (ttp-110) outliers start: 45 outliers final: 20 residues processed: 217 average time/residue: 0.2564 time to fit residues: 81.0383 Evaluate side-chains 144 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 261 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 93 optimal weight: 50.0000 chunk 145 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 209 GLN A 257 GLN A 322 GLN B 190 HIS B 209 GLN B 257 GLN B 322 GLN C 190 HIS C 209 GLN C 257 GLN C 322 GLN D 190 HIS D 209 GLN D 257 GLN D 322 GLN E 190 HIS E 209 GLN E 257 GLN E 322 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13385 Z= 0.341 Angle : 0.710 9.270 18150 Z= 0.354 Chirality : 0.042 0.153 1990 Planarity : 0.004 0.057 2370 Dihedral : 6.711 64.110 1882 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 2.50 % Allowed : 12.06 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1625 helix: 0.98 (0.17), residues: 925 sheet: -1.26 (0.35), residues: 200 loop : -2.65 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 57 HIS 0.015 0.003 HIS C 190 PHE 0.008 0.001 PHE D 282 TYR 0.011 0.001 TYR B 151 ARG 0.008 0.000 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.673 Fit side-chains REVERT: A 266 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7610 (tm-30) REVERT: A 270 ARG cc_start: 0.8205 (tpp-160) cc_final: 0.7914 (ttp-170) REVERT: B 270 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7909 (ttp-110) REVERT: C 270 ARG cc_start: 0.8219 (tpp-160) cc_final: 0.7950 (ttp-110) REVERT: D 233 ASN cc_start: 0.9154 (t0) cc_final: 0.8930 (t0) REVERT: E 270 ARG cc_start: 0.8186 (tpp-160) cc_final: 0.7917 (ttp-170) outliers start: 34 outliers final: 18 residues processed: 169 average time/residue: 0.2778 time to fit residues: 69.0590 Evaluate side-chains 147 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 ARG Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 261 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 322 GLN B 322 GLN C 322 GLN D 322 GLN E 322 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13385 Z= 0.253 Angle : 0.651 9.030 18150 Z= 0.323 Chirality : 0.041 0.159 1990 Planarity : 0.004 0.060 2370 Dihedral : 5.642 42.492 1870 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 1.18 % Allowed : 16.10 % Favored : 82.72 % 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: 0.00 (0.21), residues: 1625 helix: 1.66 (0.17), residues: 930 sheet: -1.57 (0.34), residues: 210 loop : -2.64 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 324 HIS 0.017 0.001 HIS A 190 PHE 0.010 0.001 PHE A 282 TYR 0.008 0.001 TYR C 151 ARG 0.006 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.481 Fit side-chains REVERT: A 270 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7966 (ttp-170) REVERT: B 270 ARG cc_start: 0.8207 (tpp-160) cc_final: 0.7881 (ttp-170) REVERT: C 266 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 270 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7950 (ttp-110) REVERT: C 324 TRP cc_start: 0.8700 (t60) cc_final: 0.8383 (t60) REVERT: D 233 ASN cc_start: 0.9151 (t0) cc_final: 0.8930 (t0) REVERT: D 260 GLU cc_start: 0.8440 (tp30) cc_final: 0.8221 (tp30) REVERT: E 219 TYR cc_start: 0.7475 (p90) cc_final: 0.7240 (p90) REVERT: E 270 ARG cc_start: 0.8184 (tpp-160) cc_final: 0.7900 (ttp-170) outliers start: 16 outliers final: 14 residues processed: 156 average time/residue: 0.2437 time to fit residues: 56.7322 Evaluate side-chains 144 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 ARG Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 261 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 0.0060 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 322 GLN C 322 GLN D 322 GLN E 190 HIS E 322 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13385 Z= 0.205 Angle : 0.618 8.859 18150 Z= 0.305 Chirality : 0.039 0.166 1990 Planarity : 0.003 0.045 2370 Dihedral : 5.001 23.847 1868 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 1.03 % Allowed : 17.79 % Favored : 81.18 % 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: 0.35 (0.22), residues: 1625 helix: 2.05 (0.17), residues: 935 sheet: -1.87 (0.33), residues: 220 loop : -2.54 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.015 0.001 HIS E 190 PHE 0.010 0.001 PHE E 282 TYR 0.018 0.001 TYR C 219 ARG 0.005 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 1.665 Fit side-chains REVERT: A 260 GLU cc_start: 0.8455 (tp30) cc_final: 0.8160 (tp30) REVERT: A 270 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7984 (ttp-170) REVERT: B 16 TYR cc_start: 0.7898 (t80) cc_final: 0.7644 (t80) REVERT: B 219 TYR cc_start: 0.7445 (p90) cc_final: 0.7220 (p90) REVERT: B 260 GLU cc_start: 0.8558 (tp30) cc_final: 0.8237 (tp30) REVERT: B 270 ARG cc_start: 0.8208 (tpp-160) cc_final: 0.7918 (ttp-170) REVERT: B 324 TRP cc_start: 0.8753 (t60) cc_final: 0.8333 (t60) REVERT: C 16 TYR cc_start: 0.7840 (t80) cc_final: 0.7614 (t80) REVERT: C 266 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7429 (tm-30) REVERT: C 270 ARG cc_start: 0.8242 (tpp-160) cc_final: 0.7966 (ttp-170) REVERT: C 324 TRP cc_start: 0.8701 (t60) cc_final: 0.8416 (t60) REVERT: D 233 ASN cc_start: 0.9129 (t0) cc_final: 0.8904 (t0) REVERT: D 260 GLU cc_start: 0.8444 (tp30) cc_final: 0.8126 (tp30) REVERT: E 16 TYR cc_start: 0.7841 (t80) cc_final: 0.7587 (t80) REVERT: E 219 TYR cc_start: 0.7423 (p90) cc_final: 0.7195 (p90) REVERT: E 270 ARG cc_start: 0.8180 (tpp-160) cc_final: 0.7961 (ttp-170) outliers start: 14 outliers final: 10 residues processed: 158 average time/residue: 0.2399 time to fit residues: 56.7051 Evaluate side-chains 144 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 211 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 0.0050 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 322 GLN C 322 GLN D 322 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13385 Z= 0.219 Angle : 0.621 10.892 18150 Z= 0.304 Chirality : 0.040 0.164 1990 Planarity : 0.003 0.037 2370 Dihedral : 4.712 22.584 1860 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 1.99 % Allowed : 17.94 % Favored : 80.07 % 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: 0.56 (0.22), residues: 1625 helix: 2.22 (0.17), residues: 935 sheet: -1.91 (0.32), residues: 220 loop : -2.41 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 324 HIS 0.001 0.001 HIS B 46 PHE 0.011 0.001 PHE E 282 TYR 0.015 0.001 TYR D 273 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.668 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: A 219 TYR cc_start: 0.7378 (p90) cc_final: 0.7153 (p90) REVERT: A 260 GLU cc_start: 0.8447 (tp30) cc_final: 0.8144 (tp30) REVERT: A 266 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 270 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7965 (ttp-170) REVERT: A 324 TRP cc_start: 0.8666 (t60) cc_final: 0.8431 (t60) REVERT: B 16 TYR cc_start: 0.7856 (t80) cc_final: 0.7580 (t80) REVERT: B 40 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: B 219 TYR cc_start: 0.7418 (p90) cc_final: 0.7169 (p90) REVERT: B 260 GLU cc_start: 0.8563 (tp30) cc_final: 0.8244 (tp30) REVERT: B 270 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7947 (ttp-170) REVERT: B 324 TRP cc_start: 0.8756 (t60) cc_final: 0.8361 (t60) REVERT: C 16 TYR cc_start: 0.7871 (t80) cc_final: 0.7621 (t80) REVERT: C 40 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: C 260 GLU cc_start: 0.8446 (tp30) cc_final: 0.8035 (tp30) REVERT: C 266 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7416 (tm-30) REVERT: C 270 ARG cc_start: 0.8255 (tpp-160) cc_final: 0.7977 (ttp-170) REVERT: C 324 TRP cc_start: 0.8693 (t60) cc_final: 0.8399 (t60) REVERT: D 40 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: D 219 TYR cc_start: 0.7458 (p90) cc_final: 0.7204 (p90) REVERT: D 233 ASN cc_start: 0.9124 (t0) cc_final: 0.8889 (t0) REVERT: E 16 TYR cc_start: 0.7846 (t80) cc_final: 0.7563 (t80) REVERT: E 219 TYR cc_start: 0.7436 (p90) cc_final: 0.7174 (p90) REVERT: E 260 GLU cc_start: 0.8480 (tp30) cc_final: 0.7990 (tp30) REVERT: E 266 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7344 (tm-30) REVERT: E 270 ARG cc_start: 0.8187 (tpp-160) cc_final: 0.7902 (ttp-170) REVERT: E 324 TRP cc_start: 0.8681 (t60) cc_final: 0.8396 (t60) outliers start: 27 outliers final: 12 residues processed: 167 average time/residue: 0.2288 time to fit residues: 57.8421 Evaluate side-chains 152 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 269 ASN B 322 GLN C 322 GLN D 322 GLN E 322 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13385 Z= 0.196 Angle : 0.601 8.403 18150 Z= 0.296 Chirality : 0.039 0.164 1990 Planarity : 0.003 0.034 2370 Dihedral : 4.636 21.910 1860 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 1.25 % Allowed : 19.56 % Favored : 79.19 % 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: 0.73 (0.22), residues: 1625 helix: 2.36 (0.17), residues: 935 sheet: -1.71 (0.32), residues: 210 loop : -2.42 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 324 HIS 0.001 0.000 HIS B 46 PHE 0.016 0.001 PHE E 321 TYR 0.014 0.001 TYR A 16 ARG 0.003 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: A 219 TYR cc_start: 0.7387 (p90) cc_final: 0.7155 (p90) REVERT: A 260 GLU cc_start: 0.8430 (tp30) cc_final: 0.8115 (tp30) REVERT: A 270 ARG cc_start: 0.8227 (tpp-160) cc_final: 0.7999 (ttp-170) REVERT: B 16 TYR cc_start: 0.7849 (t80) cc_final: 0.7572 (t80) REVERT: B 40 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: B 219 TYR cc_start: 0.7411 (p90) cc_final: 0.7143 (p90) REVERT: B 260 GLU cc_start: 0.8562 (tp30) cc_final: 0.8247 (tp30) REVERT: B 270 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7986 (ttp-170) REVERT: B 324 TRP cc_start: 0.8744 (t60) cc_final: 0.8379 (t60) REVERT: C 16 TYR cc_start: 0.7838 (t80) cc_final: 0.7578 (t80) REVERT: C 40 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: C 260 GLU cc_start: 0.8437 (tp30) cc_final: 0.8007 (tp30) REVERT: C 266 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7377 (tm-30) REVERT: C 270 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7966 (ttp-170) REVERT: C 324 TRP cc_start: 0.8683 (t60) cc_final: 0.8424 (t60) REVERT: D 40 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: D 219 TYR cc_start: 0.7453 (p90) cc_final: 0.7177 (p90) REVERT: D 233 ASN cc_start: 0.9115 (t0) cc_final: 0.8884 (t0) REVERT: D 270 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7709 (ttp-110) REVERT: E 16 TYR cc_start: 0.7834 (t80) cc_final: 0.7538 (t80) REVERT: E 219 TYR cc_start: 0.7399 (p90) cc_final: 0.7130 (p90) REVERT: E 260 GLU cc_start: 0.8472 (tp30) cc_final: 0.7980 (tp30) REVERT: E 266 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7332 (tm-30) REVERT: E 270 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7942 (ttp-170) REVERT: E 324 TRP cc_start: 0.8705 (t60) cc_final: 0.8426 (t60) outliers start: 17 outliers final: 9 residues processed: 161 average time/residue: 0.2297 time to fit residues: 55.4074 Evaluate side-chains 149 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 71 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 322 GLN B 322 GLN C 322 GLN D 269 ASN D 322 GLN E 269 ASN E 322 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13385 Z= 0.160 Angle : 0.580 9.190 18150 Z= 0.286 Chirality : 0.038 0.163 1990 Planarity : 0.003 0.032 2370 Dihedral : 4.460 21.225 1860 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.69 % Allowed : 18.90 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1625 helix: 2.55 (0.17), residues: 935 sheet: -1.96 (0.30), residues: 220 loop : -2.26 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 324 HIS 0.001 0.000 HIS B 155 PHE 0.012 0.001 PHE E 321 TYR 0.005 0.001 TYR D 16 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: A 219 TYR cc_start: 0.7331 (p90) cc_final: 0.7083 (p90) REVERT: A 260 GLU cc_start: 0.8407 (tp30) cc_final: 0.8099 (tp30) REVERT: A 270 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7961 (ttp-170) REVERT: B 16 TYR cc_start: 0.7829 (t80) cc_final: 0.7552 (t80) REVERT: B 40 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: B 64 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7615 (tt) REVERT: B 219 TYR cc_start: 0.7393 (p90) cc_final: 0.7138 (p90) REVERT: B 260 GLU cc_start: 0.8549 (tp30) cc_final: 0.8249 (tp30) REVERT: B 266 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7266 (tm-30) REVERT: B 270 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.7843 (ttm170) REVERT: B 324 TRP cc_start: 0.8720 (t60) cc_final: 0.8402 (t60) REVERT: C 16 TYR cc_start: 0.7798 (t80) cc_final: 0.7539 (t80) REVERT: C 40 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: C 260 GLU cc_start: 0.8411 (tp30) cc_final: 0.7959 (tp30) REVERT: C 266 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7306 (tm-30) REVERT: C 270 ARG cc_start: 0.8261 (tpp-160) cc_final: 0.7996 (ttp-170) REVERT: C 323 TRP cc_start: 0.6828 (m100) cc_final: 0.6567 (m100) REVERT: C 324 TRP cc_start: 0.8670 (t60) cc_final: 0.8449 (t60) REVERT: D 16 TYR cc_start: 0.7907 (t80) cc_final: 0.7650 (t80) REVERT: D 40 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: D 64 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7546 (tt) REVERT: D 219 TYR cc_start: 0.7464 (p90) cc_final: 0.7199 (p90) REVERT: D 233 ASN cc_start: 0.9064 (t0) cc_final: 0.8827 (t0) REVERT: D 270 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7705 (ttp-110) REVERT: E 16 TYR cc_start: 0.7825 (t80) cc_final: 0.7527 (t80) REVERT: E 219 TYR cc_start: 0.7400 (p90) cc_final: 0.7131 (p90) REVERT: E 266 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7241 (tm-30) REVERT: E 270 ARG cc_start: 0.8220 (tpp-160) cc_final: 0.7932 (ttm170) REVERT: E 324 TRP cc_start: 0.8701 (t60) cc_final: 0.8467 (t60) outliers start: 23 outliers final: 10 residues processed: 181 average time/residue: 0.2378 time to fit residues: 64.5202 Evaluate side-chains 167 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 29 optimal weight: 0.3980 chunk 98 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 322 GLN C 322 GLN D 322 GLN E 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13385 Z= 0.195 Angle : 0.602 9.116 18150 Z= 0.297 Chirality : 0.039 0.183 1990 Planarity : 0.003 0.030 2370 Dihedral : 4.506 20.863 1860 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.96 % Allowed : 20.00 % Favored : 79.04 % 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: 0.91 (0.22), residues: 1625 helix: 2.53 (0.17), residues: 935 sheet: -1.91 (0.30), residues: 220 loop : -2.25 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 324 HIS 0.001 0.000 HIS C 46 PHE 0.011 0.001 PHE E 321 TYR 0.009 0.001 TYR B 14 ARG 0.003 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: A 219 TYR cc_start: 0.7347 (p90) cc_final: 0.7091 (p90) REVERT: A 260 GLU cc_start: 0.8413 (tp30) cc_final: 0.8095 (tp30) REVERT: A 270 ARG cc_start: 0.8239 (tpp-160) cc_final: 0.7982 (ttp-170) REVERT: B 16 TYR cc_start: 0.7854 (t80) cc_final: 0.7549 (t80) REVERT: B 40 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: B 219 TYR cc_start: 0.7388 (p90) cc_final: 0.7105 (p90) REVERT: B 260 GLU cc_start: 0.8557 (tp30) cc_final: 0.8235 (tp30) REVERT: B 266 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 270 ARG cc_start: 0.8243 (tpp-160) cc_final: 0.7891 (ttm170) REVERT: B 324 TRP cc_start: 0.8725 (t60) cc_final: 0.8410 (t60) REVERT: C 16 TYR cc_start: 0.7822 (t80) cc_final: 0.7531 (t80) REVERT: C 40 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: C 260 GLU cc_start: 0.8414 (tp30) cc_final: 0.7953 (tp30) REVERT: C 266 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7324 (tm-30) REVERT: C 270 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.8006 (ttp-170) REVERT: C 323 TRP cc_start: 0.6766 (m100) cc_final: 0.6491 (m100) REVERT: C 324 TRP cc_start: 0.8685 (t60) cc_final: 0.8456 (t60) REVERT: D 16 TYR cc_start: 0.7878 (t80) cc_final: 0.7584 (t80) REVERT: D 40 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: D 219 TYR cc_start: 0.7472 (p90) cc_final: 0.7181 (p90) REVERT: D 233 ASN cc_start: 0.9084 (t0) cc_final: 0.8878 (t0) REVERT: D 324 TRP cc_start: 0.8734 (t60) cc_final: 0.8460 (t60) REVERT: E 16 TYR cc_start: 0.7837 (t80) cc_final: 0.7521 (t80) REVERT: E 219 TYR cc_start: 0.7462 (p90) cc_final: 0.7198 (p90) REVERT: E 260 GLU cc_start: 0.8457 (tp30) cc_final: 0.8053 (tp30) REVERT: E 266 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7253 (tm-30) REVERT: E 270 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7947 (ttp-170) REVERT: E 324 TRP cc_start: 0.8706 (t60) cc_final: 0.8470 (t60) outliers start: 13 outliers final: 8 residues processed: 162 average time/residue: 0.2655 time to fit residues: 64.2699 Evaluate side-chains 158 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 322 GLN C 322 GLN D 322 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13385 Z= 0.275 Angle : 0.640 9.963 18150 Z= 0.316 Chirality : 0.040 0.171 1990 Planarity : 0.003 0.032 2370 Dihedral : 4.681 21.643 1860 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 1.03 % Allowed : 20.15 % Favored : 78.82 % 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: 0.81 (0.22), residues: 1625 helix: 2.41 (0.17), residues: 935 sheet: -1.35 (0.33), residues: 185 loop : -2.48 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 324 HIS 0.002 0.001 HIS A 46 PHE 0.011 0.001 PHE E 321 TYR 0.010 0.001 TYR B 151 ARG 0.003 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.7405 (p90) cc_final: 0.7157 (p90) REVERT: A 260 GLU cc_start: 0.8447 (tp30) cc_final: 0.8123 (tp30) REVERT: A 270 ARG cc_start: 0.8245 (tpp-160) cc_final: 0.7990 (ttp-170) REVERT: B 16 TYR cc_start: 0.7902 (t80) cc_final: 0.7575 (t80) REVERT: B 40 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: B 219 TYR cc_start: 0.7425 (p90) cc_final: 0.7142 (p90) REVERT: B 260 GLU cc_start: 0.8564 (tp30) cc_final: 0.8205 (tp30) REVERT: B 266 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7338 (tm-30) REVERT: B 270 ARG cc_start: 0.8240 (tpp-160) cc_final: 0.7909 (ttp-170) REVERT: B 324 TRP cc_start: 0.8743 (t60) cc_final: 0.8434 (t60) REVERT: C 16 TYR cc_start: 0.7845 (t80) cc_final: 0.7534 (t80) REVERT: C 40 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: C 260 GLU cc_start: 0.8420 (tp30) cc_final: 0.7989 (tp30) REVERT: C 266 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7359 (tm-30) REVERT: C 270 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.8003 (ttp-170) REVERT: C 324 TRP cc_start: 0.8712 (t60) cc_final: 0.8445 (t60) REVERT: D 16 TYR cc_start: 0.7896 (t80) cc_final: 0.7583 (t80) REVERT: D 40 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: D 219 TYR cc_start: 0.7497 (p90) cc_final: 0.7209 (p90) REVERT: D 233 ASN cc_start: 0.9141 (t0) cc_final: 0.8903 (t0) REVERT: D 266 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: E 16 TYR cc_start: 0.7873 (t80) cc_final: 0.7537 (t80) REVERT: E 219 TYR cc_start: 0.7509 (p90) cc_final: 0.7216 (p90) REVERT: E 266 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7307 (tm-30) REVERT: E 270 ARG cc_start: 0.8227 (tpp-160) cc_final: 0.7939 (ttm170) REVERT: E 324 TRP cc_start: 0.8697 (t60) cc_final: 0.8430 (t60) outliers start: 14 outliers final: 9 residues processed: 158 average time/residue: 0.2428 time to fit residues: 57.1284 Evaluate side-chains 153 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.8980 chunk 92 optimal weight: 0.0870 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 126 optimal weight: 20.0000 chunk 13 optimal weight: 0.0000 chunk 98 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 322 GLN C 269 ASN C 322 GLN D 322 GLN E 322 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13385 Z= 0.162 Angle : 0.589 8.706 18150 Z= 0.292 Chirality : 0.038 0.167 1990 Planarity : 0.003 0.030 2370 Dihedral : 4.460 21.072 1860 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.88 % Allowed : 20.37 % Favored : 78.75 % 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: 1.02 (0.22), residues: 1625 helix: 2.67 (0.17), residues: 930 sheet: -1.92 (0.30), residues: 220 loop : -2.23 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 324 HIS 0.001 0.000 HIS C 46 PHE 0.016 0.001 PHE B 321 TYR 0.006 0.001 TYR A 16 ARG 0.003 0.000 ARG B 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.7324 (p90) cc_final: 0.7064 (p90) REVERT: A 260 GLU cc_start: 0.8406 (tp30) cc_final: 0.8096 (tp30) REVERT: A 270 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.7969 (ttp-170) REVERT: B 16 TYR cc_start: 0.7858 (t80) cc_final: 0.7578 (t80) REVERT: B 40 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: B 219 TYR cc_start: 0.7357 (p90) cc_final: 0.7053 (p90) REVERT: B 260 GLU cc_start: 0.8552 (tp30) cc_final: 0.8247 (tp30) REVERT: B 266 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7215 (tm-30) REVERT: B 270 ARG cc_start: 0.8231 (tpp-160) cc_final: 0.7874 (ttm170) REVERT: B 324 TRP cc_start: 0.8731 (t60) cc_final: 0.8443 (t60) REVERT: C 16 TYR cc_start: 0.7780 (t80) cc_final: 0.7506 (t80) REVERT: C 260 GLU cc_start: 0.8385 (tp30) cc_final: 0.7920 (tp30) REVERT: C 266 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7282 (tm-30) REVERT: C 270 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7999 (ttm170) REVERT: C 323 TRP cc_start: 0.6814 (m100) cc_final: 0.6568 (m100) REVERT: C 324 TRP cc_start: 0.8687 (t60) cc_final: 0.8454 (t60) REVERT: D 16 TYR cc_start: 0.7853 (t80) cc_final: 0.7565 (t80) REVERT: D 219 TYR cc_start: 0.7432 (p90) cc_final: 0.7135 (p90) REVERT: D 233 ASN cc_start: 0.9063 (t0) cc_final: 0.8829 (t0) REVERT: D 266 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: E 16 TYR cc_start: 0.7829 (t80) cc_final: 0.7522 (t80) REVERT: E 219 TYR cc_start: 0.7452 (p90) cc_final: 0.7158 (p90) REVERT: E 266 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7250 (tm-30) REVERT: E 270 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7932 (ttm170) REVERT: E 324 TRP cc_start: 0.8700 (t60) cc_final: 0.8478 (t60) outliers start: 12 outliers final: 9 residues processed: 157 average time/residue: 0.2512 time to fit residues: 57.8894 Evaluate side-chains 153 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.0060 chunk 117 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 322 GLN C 322 GLN D 322 GLN E 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.111780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.084274 restraints weight = 29119.951| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.97 r_work: 0.3195 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13385 Z= 0.155 Angle : 0.575 7.872 18150 Z= 0.285 Chirality : 0.038 0.159 1990 Planarity : 0.003 0.030 2370 Dihedral : 4.341 20.137 1860 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.96 % Allowed : 20.00 % Favored : 79.04 % 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: 1.15 (0.22), residues: 1625 helix: 2.76 (0.17), residues: 930 sheet: -1.89 (0.30), residues: 220 loop : -2.14 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 324 HIS 0.001 0.000 HIS C 46 PHE 0.013 0.001 PHE E 281 TYR 0.005 0.001 TYR A 16 ARG 0.003 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3028.31 seconds wall clock time: 55 minutes 37.85 seconds (3337.85 seconds total)