Starting phenix.real_space_refine on Tue Apr 9 17:36:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/04_2024/8tzk_41761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/04_2024/8tzk_41761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/04_2024/8tzk_41761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/04_2024/8tzk_41761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/04_2024/8tzk_41761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/04_2024/8tzk_41761_updated.pdb" } resolution = 3.55 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= 0.017 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 5491 2.51 5 N 1550 2.21 5 O 1535 1.98 5 H 8468 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17077 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3494 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3494 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4369 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 10, 'ASP:plan': 9, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 4359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4359 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1305 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 88 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.67, per 1000 atoms: 0.45 Number of scatterers: 17077 At special positions: 0 Unit cell: (105.84, 83.16, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 27 16.00 P 4 15.00 Mg 2 11.99 O 1535 8.00 N 1550 7.00 C 5491 6.00 H 8468 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: 13.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 6 sheets defined 57.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 50 through 57 Processing helix chain 'A' and resid 83 through 89 removed outlier: 3.784A pdb=" N ASN A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Proline residue: A 112 - end of helix removed outlier: 3.739A pdb=" N GLU A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.709A pdb=" N ARG A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 83 through 89 removed outlier: 3.766A pdb=" N ASN B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 116 Proline residue: B 112 - end of helix removed outlier: 3.759A pdb=" N GLU B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 149 through 161 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.671A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'C' and resid 32 through 85 removed outlier: 3.629A pdb=" N HIS C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Proline residue: C 51 - end of helix removed outlier: 3.604A pdb=" N THR C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Proline residue: C 68 - end of helix Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.898A pdb=" N ILE C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 135 Processing helix chain 'C' and resid 163 through 177 Processing helix chain 'C' and resid 198 through 239 removed outlier: 3.868A pdb=" N GLY C 219 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 286 Proline residue: C 249 - end of helix removed outlier: 4.651A pdb=" N GLY C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 324 removed outlier: 3.909A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 48 removed outlier: 3.529A pdb=" N HIS D 36 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TRP D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 86 Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 189 through 228 removed outlier: 3.624A pdb=" N GLY D 219 " --> pdb=" O PHE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 238 Processing helix chain 'D' and resid 243 through 285 Proline residue: D 249 - end of helix removed outlier: 3.727A pdb=" N LEU D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 324 removed outlier: 3.632A pdb=" N LEU D 302 " --> pdb=" O TRP D 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 128 removed outlier: 3.632A pdb=" N ARG E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 190 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 removed outlier: 3.529A pdb=" N LYS A 67 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.665A pdb=" N LEU A 167 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL A 93 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 169 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR A 198 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA A 170 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 200 " --> pdb=" O ALA A 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 12 through 14 removed outlier: 3.508A pdb=" N LYS B 67 " --> pdb=" O GLN B 14 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.649A pdb=" N LEU B 167 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL B 93 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 169 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 198 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA B 170 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 200 " --> pdb=" O ALA B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.633A pdb=" N VAL C 153 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.612A pdb=" N ASP D 181 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 153 " --> pdb=" O ILE D 123 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1491 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: 5.86 Time building geometry restraints manager: 13.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8462 1.03 - 1.23: 6 1.23 - 1.42: 3534 1.42 - 1.61: 5162 1.61 - 1.81: 54 Bond restraints: 17218 Sorted by residual: bond pdb=" C6 ADP A 302 " pdb=" N6 ADP A 302 " ideal model delta sigma weight residual 1.355 1.450 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C6 ADP B 302 " pdb=" N6 ADP B 302 " ideal model delta sigma weight residual 1.355 1.449 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C4 ADP A 302 " pdb=" C5 ADP A 302 " ideal model delta sigma weight residual 1.490 1.397 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C4 ADP B 302 " pdb=" C5 ADP B 302 " ideal model delta sigma weight residual 1.490 1.397 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" O3A ADP B 302 " pdb=" PB ADP B 302 " ideal model delta sigma weight residual 1.610 1.684 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 17213 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.34: 1792 107.34 - 114.11: 19164 114.11 - 120.87: 6409 120.87 - 127.63: 3676 127.63 - 134.39: 75 Bond angle restraints: 31116 Sorted by residual: angle pdb=" O2B ADP B 302 " pdb=" PB ADP B 302 " pdb=" O3B ADP B 302 " ideal model delta sigma weight residual 119.90 109.35 10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O2B ADP A 302 " pdb=" PB ADP A 302 " pdb=" O3B ADP A 302 " ideal model delta sigma weight residual 119.90 109.45 10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N ILE D 239 " pdb=" CA ILE D 239 " pdb=" C ILE D 239 " ideal model delta sigma weight residual 110.21 106.30 3.91 1.13e+00 7.83e-01 1.20e+01 angle pdb=" O1B ADP B 302 " pdb=" PB ADP B 302 " pdb=" O3B ADP B 302 " ideal model delta sigma weight residual 119.90 109.67 10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" O1B ADP B 302 " pdb=" PB ADP B 302 " pdb=" O2B ADP B 302 " ideal model delta sigma weight residual 119.90 109.72 10.18 3.00e+00 1.11e-01 1.15e+01 ... (remaining 31111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 7770 24.87 - 49.73: 219 49.73 - 74.60: 65 74.60 - 99.46: 1 99.46 - 124.33: 6 Dihedral angle restraints: 8061 sinusoidal: 4289 harmonic: 3772 Sorted by residual: dihedral pdb=" O2A ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PA ADP B 302 " pdb=" PB ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 64.33 -124.33 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" O1B ADP A 302 " pdb=" O3A ADP A 302 " pdb=" PB ADP A 302 " pdb=" PA ADP A 302 " ideal model delta sinusoidal sigma weight residual -60.00 61.90 -121.90 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1B ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PB ADP B 302 " pdb=" PA ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 59.60 -119.60 1 2.00e+01 2.50e-03 3.59e+01 ... (remaining 8058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1173 0.042 - 0.084: 179 0.084 - 0.126: 61 0.126 - 0.168: 5 0.168 - 0.211: 6 Chirality restraints: 1424 Sorted by residual: chirality pdb=" C2' ADP A 302 " pdb=" C1' ADP A 302 " pdb=" C3' ADP A 302 " pdb=" O2' ADP A 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' ADP A 302 " pdb=" C2' ADP A 302 " pdb=" C4' ADP A 302 " pdb=" O3' ADP A 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' ADP B 302 " pdb=" C2' ADP B 302 " pdb=" C4' ADP B 302 " pdb=" O3' ADP B 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1421 not shown) Planarity restraints: 2615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 87 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.24e-01 pdb=" N PRO C 88 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 212 " 0.013 5.00e-02 4.00e+02 2.02e-02 6.54e-01 pdb=" N PRO B 213 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 101 " 0.012 5.00e-02 4.00e+02 1.84e-02 5.40e-01 pdb=" N PRO C 102 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.010 5.00e-02 4.00e+02 ... (remaining 2612 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 400 2.13 - 2.75: 31452 2.75 - 3.36: 46267 3.36 - 3.98: 55886 3.98 - 4.60: 90382 Nonbonded interactions: 224387 Sorted by model distance: nonbonded pdb=" O GLU B 116 " pdb=" HG SER B 117 " model vdw 1.511 1.850 nonbonded pdb=" O LEU E 122 " pdb=" HG1 THR E 125 " model vdw 1.588 1.850 nonbonded pdb=" O GLU A 116 " pdb=" HG SER A 117 " model vdw 1.623 1.850 nonbonded pdb=" HD1 HIS D 36 " pdb=" OH TYR D 252 " model vdw 1.643 1.850 nonbonded pdb="HE21 GLN A 25 " pdb=" OE1 GLN A 28 " model vdw 1.668 1.850 ... (remaining 224382 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' } ncs_group { reference = (chain 'C' and (resid 27 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 85 through 91 or (resid \ 92 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 93 through 99 or (resid 100 and (name N or name CA or name C or name O \ or name CB or name HA )) or resid 101 or (resid 102 and (name N or name CA or n \ ame C or name O or name CB or name HA )) or (resid 103 through 117 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 118 th \ rough 120 or (resid 121 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 122 through 123 or (resid 124 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 125 through \ 152 or (resid 153 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 154 or (resid 155 through 157 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or (resid 158 and (name N o \ r name CA or name C or name O or name CB or name HA )) or resid 159 through 230 \ or (resid 231 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 232 through 241 or (resid 242 through 243 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 244 throug \ h 291 or (resid 292 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 293 or (resid 294 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 295 through 330)) selection = (chain 'D' and (resid 27 or (resid 28 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 29 through 35 or (resid 36 and (nam \ e N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD \ 2 or name HE1 or name HE2)) or resid 37 through 82 or (resid 83 through 84 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 85 through 89 or (resid 90 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 91 through 94 or (resid 95 through 96 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 97 through 110 or (resid 111 through 117 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 118 through 148 or (resid 149 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 150 through 162 or (resid 163 through 169 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 170 through 172 or (resid \ 173 through 174 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 175 through 178 or (resid 179 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 180 or (resid 181 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 182 through 183 or (resid 184 through 187 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 188 through 191 or (resid \ 192 through 193 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 194 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 197 through 287 or \ (resid 288 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 289 through 330)) } 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: 5.020 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: 0.250 Extract box with map and model: 20.660 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 54.700 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.004 0.095 8750 Z= 0.268 Angle : 0.527 10.553 11890 Z= 0.246 Chirality : 0.037 0.211 1424 Planarity : 0.002 0.021 1509 Dihedral : 11.132 124.329 3110 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 3.24 (0.26), residues: 1139 helix: 3.71 (0.19), residues: 672 sheet: 0.47 (0.56), residues: 103 loop : -0.50 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.002 0.001 HIS B 97 PHE 0.006 0.001 PHE C 257 TYR 0.008 0.001 TYR D 252 ARG 0.003 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8660 (mmm) cc_final: 0.8317 (mmt) REVERT: C 41 LYS cc_start: 0.8721 (tttt) cc_final: 0.8507 (ttmm) REVERT: C 63 MET cc_start: 0.8253 (mtm) cc_final: 0.7980 (mtt) REVERT: D 223 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7216 (ttp-170) REVERT: E 123 LEU cc_start: 0.9022 (tt) cc_final: 0.8536 (mt) REVERT: E 141 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7580 (tpm170) REVERT: E 170 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8416 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.6517 time to fit residues: 159.3805 Evaluate side-chains 114 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 80 ASN E 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8750 Z= 0.187 Angle : 0.526 6.692 11890 Z= 0.257 Chirality : 0.036 0.165 1424 Planarity : 0.003 0.025 1509 Dihedral : 8.099 136.171 1262 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.08 % Allowed : 8.19 % Favored : 90.72 % 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: 3.12 (0.26), residues: 1139 helix: 3.63 (0.19), residues: 673 sheet: 0.17 (0.54), residues: 103 loop : -0.52 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 298 HIS 0.002 0.001 HIS B 97 PHE 0.017 0.001 PHE C 215 TYR 0.009 0.001 TYR A 106 ARG 0.004 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7588 (mt-10) REVERT: B 101 MET cc_start: 0.8657 (mmm) cc_final: 0.8357 (mmt) REVERT: C 41 LYS cc_start: 0.8720 (tttt) cc_final: 0.8504 (ttmm) REVERT: D 223 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.7255 (ttp-170) REVERT: D 306 MET cc_start: 0.6636 (tmm) cc_final: 0.6406 (tmm) REVERT: E 123 LEU cc_start: 0.9032 (tt) cc_final: 0.8524 (mt) REVERT: E 141 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7607 (tpm170) REVERT: E 170 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8393 (tm-30) outliers start: 9 outliers final: 7 residues processed: 134 average time/residue: 0.5889 time to fit residues: 102.0927 Evaluate side-chains 119 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8750 Z= 0.189 Angle : 0.500 6.134 11890 Z= 0.249 Chirality : 0.036 0.152 1424 Planarity : 0.003 0.025 1509 Dihedral : 7.566 137.118 1262 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.33 % Allowed : 9.40 % Favored : 89.28 % 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: 3.05 (0.25), residues: 1139 helix: 3.59 (0.19), residues: 677 sheet: 0.34 (0.61), residues: 78 loop : -0.66 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.002 0.001 HIS A 33 PHE 0.023 0.001 PHE C 291 TYR 0.009 0.001 TYR D 252 ARG 0.006 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 101 MET cc_start: 0.8637 (mmm) cc_final: 0.8346 (mmt) REVERT: D 223 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.7214 (ttp-170) REVERT: D 306 MET cc_start: 0.6682 (tmm) cc_final: 0.6438 (tmm) REVERT: E 120 GLU cc_start: 0.8059 (tp30) cc_final: 0.7760 (tp30) REVERT: E 123 LEU cc_start: 0.9019 (tt) cc_final: 0.8516 (mt) REVERT: E 141 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7611 (tpm170) REVERT: E 170 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8462 (tm-30) outliers start: 11 outliers final: 10 residues processed: 123 average time/residue: 0.5941 time to fit residues: 94.3803 Evaluate side-chains 121 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8750 Z= 0.233 Angle : 0.508 5.999 11890 Z= 0.255 Chirality : 0.036 0.156 1424 Planarity : 0.003 0.024 1509 Dihedral : 7.223 135.807 1262 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.69 % Allowed : 8.80 % Favored : 89.52 % 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: 2.86 (0.25), residues: 1139 helix: 3.44 (0.19), residues: 679 sheet: 0.23 (0.61), residues: 80 loop : -0.74 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.002 0.001 HIS A 33 PHE 0.008 0.001 PHE A 32 TYR 0.010 0.001 TYR D 250 ARG 0.003 0.000 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 101 MET cc_start: 0.8655 (mmm) cc_final: 0.8367 (mmt) REVERT: C 291 PHE cc_start: 0.7301 (t80) cc_final: 0.6723 (t80) REVERT: D 306 MET cc_start: 0.6717 (tmm) cc_final: 0.6449 (tmm) REVERT: E 120 GLU cc_start: 0.8185 (tp30) cc_final: 0.7800 (tp30) REVERT: E 123 LEU cc_start: 0.9030 (tt) cc_final: 0.8524 (mt) REVERT: E 141 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7609 (tpm170) REVERT: E 170 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8455 (tm-30) outliers start: 14 outliers final: 11 residues processed: 123 average time/residue: 0.6053 time to fit residues: 98.6521 Evaluate side-chains 123 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN E 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8750 Z= 0.278 Angle : 0.523 6.185 11890 Z= 0.266 Chirality : 0.037 0.162 1424 Planarity : 0.003 0.027 1509 Dihedral : 7.263 142.611 1262 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.93 % Allowed : 9.52 % Favored : 88.55 % 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: 2.64 (0.25), residues: 1139 helix: 3.28 (0.19), residues: 677 sheet: -0.00 (0.60), residues: 80 loop : -0.81 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.004 0.001 HIS B 73 PHE 0.011 0.001 PHE A 32 TYR 0.011 0.002 TYR E 151 ARG 0.004 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 101 MET cc_start: 0.8689 (mmm) cc_final: 0.8411 (mmt) REVERT: D 306 MET cc_start: 0.6771 (tmm) cc_final: 0.6465 (tmm) REVERT: E 123 LEU cc_start: 0.9023 (tt) cc_final: 0.8546 (mt) REVERT: E 141 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7634 (tpm170) REVERT: E 170 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8423 (tm-30) outliers start: 16 outliers final: 13 residues processed: 124 average time/residue: 0.5663 time to fit residues: 91.8314 Evaluate side-chains 121 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8750 Z= 0.238 Angle : 0.508 6.144 11890 Z= 0.257 Chirality : 0.037 0.167 1424 Planarity : 0.003 0.050 1509 Dihedral : 7.251 145.535 1262 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.69 % Allowed : 10.36 % Favored : 87.95 % 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: 2.63 (0.25), residues: 1139 helix: 3.26 (0.19), residues: 678 sheet: -0.09 (0.60), residues: 80 loop : -0.80 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.003 0.001 HIS A 33 PHE 0.009 0.001 PHE A 32 TYR 0.011 0.001 TYR C 250 ARG 0.004 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7626 (mt-10) REVERT: B 101 MET cc_start: 0.8684 (mmm) cc_final: 0.8371 (mmt) REVERT: C 291 PHE cc_start: 0.7289 (t80) cc_final: 0.6771 (t80) REVERT: D 140 GLN cc_start: 0.8805 (mp10) cc_final: 0.8592 (mp10) REVERT: D 306 MET cc_start: 0.6858 (tmm) cc_final: 0.6519 (tmm) REVERT: D 326 GLU cc_start: 0.8542 (pp20) cc_final: 0.8280 (pp20) REVERT: E 123 LEU cc_start: 0.9023 (tt) cc_final: 0.8550 (mt) REVERT: E 141 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7672 (tpm170) REVERT: E 170 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8425 (tm-30) outliers start: 14 outliers final: 12 residues processed: 121 average time/residue: 0.5755 time to fit residues: 90.8816 Evaluate side-chains 123 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 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 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8750 Z= 0.238 Angle : 0.508 6.191 11890 Z= 0.256 Chirality : 0.037 0.167 1424 Planarity : 0.003 0.029 1509 Dihedral : 7.253 147.534 1262 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.81 % Allowed : 10.84 % Favored : 87.35 % 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: 2.63 (0.25), residues: 1139 helix: 3.28 (0.19), residues: 673 sheet: -0.14 (0.60), residues: 80 loop : -0.76 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.001 PHE A 32 TYR 0.010 0.001 TYR D 250 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7631 (mt-10) REVERT: B 101 MET cc_start: 0.8683 (mmm) cc_final: 0.8360 (mmt) REVERT: C 291 PHE cc_start: 0.7326 (t80) cc_final: 0.6806 (t80) REVERT: D 306 MET cc_start: 0.6850 (tmm) cc_final: 0.6505 (tmm) REVERT: D 326 GLU cc_start: 0.8578 (pp20) cc_final: 0.8287 (pp20) REVERT: E 123 LEU cc_start: 0.9025 (tt) cc_final: 0.8557 (mt) REVERT: E 141 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7680 (tpm170) REVERT: E 170 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8430 (tm-30) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 0.5813 time to fit residues: 93.5700 Evaluate side-chains 121 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8750 Z= 0.302 Angle : 0.535 5.926 11890 Z= 0.274 Chirality : 0.037 0.161 1424 Planarity : 0.003 0.030 1509 Dihedral : 7.421 150.155 1262 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.69 % Allowed : 10.60 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.25), residues: 1139 helix: 3.16 (0.19), residues: 673 sheet: -0.27 (0.60), residues: 80 loop : -0.89 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 298 HIS 0.004 0.001 HIS B 73 PHE 0.013 0.001 PHE A 32 TYR 0.011 0.001 TYR C 250 ARG 0.004 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7680 (mt-10) REVERT: B 101 MET cc_start: 0.8731 (mmm) cc_final: 0.8407 (mmt) REVERT: C 291 PHE cc_start: 0.7358 (t80) cc_final: 0.6861 (t80) REVERT: D 326 GLU cc_start: 0.8613 (pp20) cc_final: 0.8292 (pp20) REVERT: E 123 LEU cc_start: 0.9020 (tt) cc_final: 0.8546 (mt) REVERT: E 141 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7673 (tpm170) REVERT: E 170 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8401 (tm-30) outliers start: 14 outliers final: 12 residues processed: 115 average time/residue: 0.5527 time to fit residues: 83.4569 Evaluate side-chains 120 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8750 Z= 0.223 Angle : 0.512 5.979 11890 Z= 0.256 Chirality : 0.037 0.167 1424 Planarity : 0.003 0.032 1509 Dihedral : 7.451 157.055 1262 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.45 % Allowed : 10.96 % Favored : 87.59 % 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: 2.56 (0.25), residues: 1139 helix: 3.26 (0.19), residues: 673 sheet: -0.28 (0.59), residues: 80 loop : -0.82 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 298 HIS 0.003 0.001 HIS A 33 PHE 0.009 0.001 PHE A 32 TYR 0.010 0.001 TYR D 250 ARG 0.004 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7634 (mt-10) REVERT: B 101 MET cc_start: 0.8684 (mmm) cc_final: 0.8370 (mmt) REVERT: C 291 PHE cc_start: 0.7387 (t80) cc_final: 0.6887 (t80) REVERT: D 306 MET cc_start: 0.6686 (tmm) cc_final: 0.6423 (tmm) REVERT: D 326 GLU cc_start: 0.8611 (pp20) cc_final: 0.8283 (pp20) REVERT: E 119 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8248 (tp) REVERT: E 120 GLU cc_start: 0.8107 (tp30) cc_final: 0.7845 (tp30) REVERT: E 123 LEU cc_start: 0.9022 (tt) cc_final: 0.8543 (mt) REVERT: E 141 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7694 (tpm170) REVERT: E 170 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8424 (tm-30) outliers start: 12 outliers final: 11 residues processed: 117 average time/residue: 0.5464 time to fit residues: 84.4302 Evaluate side-chains 120 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 30.0000 chunk 104 optimal weight: 30.0000 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8750 Z= 0.236 Angle : 0.516 5.869 11890 Z= 0.259 Chirality : 0.036 0.169 1424 Planarity : 0.003 0.031 1509 Dihedral : 7.625 167.534 1262 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.45 % Allowed : 11.45 % Favored : 87.11 % 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: 2.56 (0.25), residues: 1139 helix: 3.28 (0.19), residues: 672 sheet: -0.35 (0.59), residues: 80 loop : -0.85 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 298 HIS 0.004 0.001 HIS A 33 PHE 0.010 0.001 PHE A 32 TYR 0.010 0.001 TYR C 250 ARG 0.005 0.000 ARG C 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7638 (mt-10) REVERT: C 291 PHE cc_start: 0.7450 (t80) cc_final: 0.6958 (t80) REVERT: D 306 MET cc_start: 0.6686 (tmm) cc_final: 0.6419 (tmm) REVERT: D 326 GLU cc_start: 0.8622 (pp20) cc_final: 0.8290 (pp20) REVERT: E 119 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8239 (tp) REVERT: E 123 LEU cc_start: 0.9023 (tt) cc_final: 0.8551 (mt) REVERT: E 141 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7699 (tpm170) REVERT: E 170 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8405 (tm-30) outliers start: 12 outliers final: 11 residues processed: 116 average time/residue: 0.5338 time to fit residues: 82.2711 Evaluate side-chains 122 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.109662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086061 restraints weight = 48699.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090106 restraints weight = 20039.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.092689 restraints weight = 11088.453| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8750 Z= 0.176 Angle : 0.495 6.361 11890 Z= 0.244 Chirality : 0.036 0.171 1424 Planarity : 0.003 0.057 1509 Dihedral : 7.738 176.532 1262 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.20 % Allowed : 11.57 % Favored : 87.23 % 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: 2.76 (0.25), residues: 1139 helix: 3.43 (0.19), residues: 672 sheet: -0.30 (0.59), residues: 80 loop : -0.72 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 298 HIS 0.003 0.001 HIS A 97 PHE 0.007 0.001 PHE A 32 TYR 0.009 0.001 TYR D 252 ARG 0.005 0.000 ARG C 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4008.86 seconds wall clock time: 72 minutes 47.05 seconds (4367.05 seconds total)