Starting phenix.real_space_refine on Thu Mar 14 14:16:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/03_2024/8e5g_27912_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/03_2024/8e5g_27912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/03_2024/8e5g_27912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/03_2024/8e5g_27912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/03_2024/8e5g_27912_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5g_27912/03_2024/8e5g_27912_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 20 7.16 5 S 55 5.16 5 C 5710 2.51 5 N 1510 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 163": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9065 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1813 Unusual residues: {'HEC': 4} Classifications: {'peptide': 220, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 211, None: 4} Not linked: pdbres="ASP A 250 " pdbres="HEC A 301 " Not linked: pdbres="HEC A 301 " pdbres="HEC A 302 " Not linked: pdbres="HEC A 302 " pdbres="HEC A 303 " Not linked: pdbres="HEC A 303 " pdbres="HEC A 304 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1813 Unusual residues: {'HEC': 4} Classifications: {'peptide': 220, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 211, None: 4} Not linked: pdbres="ASP B 250 " pdbres="HEC B 301 " Not linked: pdbres="HEC B 301 " pdbres="HEC B 302 " Not linked: pdbres="HEC B 302 " pdbres="HEC B 303 " Not linked: pdbres="HEC B 303 " pdbres="HEC B 304 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1813 Unusual residues: {'HEC': 4} Classifications: {'peptide': 220, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 211, None: 4} Not linked: pdbres="ASP C 250 " pdbres="HEC C 301 " Not linked: pdbres="HEC C 301 " pdbres="HEC C 302 " Not linked: pdbres="HEC C 302 " pdbres="HEC C 303 " Not linked: pdbres="HEC C 303 " pdbres="HEC C 304 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1813 Unusual residues: {'HEC': 4} Classifications: {'peptide': 220, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 211, None: 4} Not linked: pdbres="ASP D 250 " pdbres="HEC D 301 " Not linked: pdbres="HEC D 301 " pdbres="HEC D 302 " Not linked: pdbres="HEC D 302 " pdbres="HEC D 303 " Not linked: pdbres="HEC D 303 " pdbres="HEC D 304 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1813 Unusual residues: {'HEC': 4} Classifications: {'peptide': 220, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 211, None: 4} Not linked: pdbres="ASP E 250 " pdbres="HEC E 301 " Not linked: pdbres="HEC E 301 " pdbres="HEC E 302 " Not linked: pdbres="HEC E 302 " pdbres="HEC E 303 " Not linked: pdbres="HEC E 303 " pdbres="HEC E 304 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.85, per 1000 atoms: 0.54 Number of scatterers: 9065 At special positions: 0 Unit cell: (84.24, 71.28, 250.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 20 26.01 S 55 16.00 O 1770 8.00 N 1510 7.00 C 5710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=71, symmetry=0 Number of additional bonds: simple=71, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 15 sheets defined 16.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.702A pdb=" N ARG A 171 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 No H-bonds generated for 'chain 'A' and resid 182 through 185' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 74 through 85 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.702A pdb=" N ARG B 171 " --> pdb=" O PHE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 No H-bonds generated for 'chain 'B' and resid 182 through 185' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 51 through 58 Processing helix chain 'C' and resid 74 through 85 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.702A pdb=" N ARG C 171 " --> pdb=" O PHE C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 185 No H-bonds generated for 'chain 'C' and resid 182 through 185' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 51 through 58 Processing helix chain 'D' and resid 74 through 85 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.702A pdb=" N ARG D 171 " --> pdb=" O PHE D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 185 No H-bonds generated for 'chain 'D' and resid 182 through 185' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 51 through 58 Processing helix chain 'E' and resid 74 through 85 Processing helix chain 'E' and resid 166 through 174 removed outlier: 3.702A pdb=" N ARG E 171 " --> pdb=" O PHE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 185 No H-bonds generated for 'chain 'E' and resid 182 through 185' Processing sheet with id= A, first strand: chain 'A' and resid 194 through 201 removed outlier: 3.508A pdb=" N HIS A 200 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 247 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 203 through 205 Processing sheet with id= C, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.551A pdb=" N ASN A 207 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 226 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 194 through 201 removed outlier: 3.508A pdb=" N HIS B 200 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 247 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= F, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.551A pdb=" N ASN B 207 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 226 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 194 through 201 removed outlier: 3.509A pdb=" N HIS C 200 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 247 " --> pdb=" O PHE C 239 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 203 through 205 Processing sheet with id= I, first strand: chain 'C' and resid 207 through 210 removed outlier: 3.551A pdb=" N ASN C 207 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 226 " --> pdb=" O ASN C 207 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 194 through 201 removed outlier: 3.508A pdb=" N HIS D 200 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 247 " --> pdb=" O PHE D 239 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 203 through 205 Processing sheet with id= L, first strand: chain 'D' and resid 207 through 210 removed outlier: 3.550A pdb=" N ASN D 207 " --> pdb=" O THR D 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 226 " --> pdb=" O ASN D 207 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 194 through 201 removed outlier: 3.509A pdb=" N HIS E 200 " --> pdb=" O ARG E 234 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER E 247 " --> pdb=" O PHE E 239 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 203 through 205 Processing sheet with id= O, first strand: chain 'E' and resid 207 through 210 removed outlier: 3.550A pdb=" N ASN E 207 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR E 226 " --> pdb=" O ASN E 207 " (cutoff:3.500A) 155 hydrogen bonds defined for protein. 345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3964 1.38 - 1.56: 5296 1.56 - 1.74: 10 1.74 - 1.91: 65 1.91 - 2.09: 80 Bond restraints: 9415 Sorted by residual: bond pdb=" N GLU B 205 " pdb=" CA GLU B 205 " ideal model delta sigma weight residual 1.457 1.557 -0.099 1.29e-02 6.01e+03 5.93e+01 bond pdb=" N GLU E 205 " pdb=" CA GLU E 205 " ideal model delta sigma weight residual 1.457 1.557 -0.099 1.29e-02 6.01e+03 5.92e+01 bond pdb=" N GLU D 205 " pdb=" CA GLU D 205 " ideal model delta sigma weight residual 1.457 1.557 -0.099 1.29e-02 6.01e+03 5.92e+01 bond pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 1.457 1.557 -0.099 1.29e-02 6.01e+03 5.91e+01 bond pdb=" N GLU C 205 " pdb=" CA GLU C 205 " ideal model delta sigma weight residual 1.457 1.556 -0.099 1.29e-02 6.01e+03 5.90e+01 ... (remaining 9410 not shown) Histogram of bond angle deviations from ideal: 87.91 - 106.22: 310 106.22 - 124.53: 11868 124.53 - 142.84: 927 142.84 - 161.15: 0 161.15 - 179.46: 40 Bond angle restraints: 13145 Sorted by residual: angle pdb=" N ASN E 207 " pdb=" CA ASN E 207 " pdb=" C ASN E 207 " ideal model delta sigma weight residual 109.29 122.67 -13.38 1.41e+00 5.03e-01 9.01e+01 angle pdb=" N ASN D 207 " pdb=" CA ASN D 207 " pdb=" C ASN D 207 " ideal model delta sigma weight residual 109.29 122.67 -13.38 1.41e+00 5.03e-01 9.00e+01 angle pdb=" N ASN A 207 " pdb=" CA ASN A 207 " pdb=" C ASN A 207 " ideal model delta sigma weight residual 109.29 122.64 -13.35 1.41e+00 5.03e-01 8.97e+01 angle pdb=" N ASN B 207 " pdb=" CA ASN B 207 " pdb=" C ASN B 207 " ideal model delta sigma weight residual 109.29 122.63 -13.34 1.41e+00 5.03e-01 8.95e+01 angle pdb=" N ASN C 207 " pdb=" CA ASN C 207 " pdb=" C ASN C 207 " ideal model delta sigma weight residual 109.29 122.62 -13.33 1.41e+00 5.03e-01 8.94e+01 ... (remaining 13140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 4280 16.78 - 33.55: 475 33.55 - 50.33: 85 50.33 - 67.10: 45 67.10 - 83.88: 40 Dihedral angle restraints: 4925 sinusoidal: 1820 harmonic: 3105 Sorted by residual: dihedral pdb=" N ASN D 207 " pdb=" C ASN D 207 " pdb=" CA ASN D 207 " pdb=" CB ASN D 207 " ideal model delta harmonic sigma weight residual 122.80 151.68 -28.88 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N ASN E 207 " pdb=" C ASN E 207 " pdb=" CA ASN E 207 " pdb=" CB ASN E 207 " ideal model delta harmonic sigma weight residual 122.80 151.65 -28.85 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N ASN A 207 " pdb=" C ASN A 207 " pdb=" CA ASN A 207 " pdb=" CB ASN A 207 " ideal model delta harmonic sigma weight residual 122.80 151.62 -28.82 0 2.50e+00 1.60e-01 1.33e+02 ... (remaining 4922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.242: 1255 0.242 - 0.484: 0 0.484 - 0.726: 5 0.726 - 0.968: 0 0.968 - 1.210: 5 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA ASN D 207 " pdb=" N ASN D 207 " pdb=" C ASN D 207 " pdb=" CB ASN D 207 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.66e+01 chirality pdb=" CA ASN E 207 " pdb=" N ASN E 207 " pdb=" C ASN E 207 " pdb=" CB ASN E 207 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.65e+01 chirality pdb=" CA ASN A 207 " pdb=" N ASN A 207 " pdb=" C ASN A 207 " pdb=" CB ASN A 207 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.64e+01 ... (remaining 1262 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 301 " -0.011 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" C2C HEC D 301 " 0.084 2.00e-02 2.50e+03 pdb=" C3C HEC D 301 " -0.001 2.00e-02 2.50e+03 pdb=" C4C HEC D 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC D 301 " -0.019 2.00e-02 2.50e+03 pdb=" CHC HEC D 301 " -0.014 2.00e-02 2.50e+03 pdb=" CHD HEC D 301 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC D 301 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC D 301 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " -0.011 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" C2C HEC C 301 " 0.084 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " -0.001 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " -0.019 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " -0.014 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC E 301 " -0.011 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" C2C HEC E 301 " 0.084 2.00e-02 2.50e+03 pdb=" C3C HEC E 301 " -0.001 2.00e-02 2.50e+03 pdb=" C4C HEC E 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC E 301 " -0.019 2.00e-02 2.50e+03 pdb=" CHC HEC E 301 " -0.014 2.00e-02 2.50e+03 pdb=" CHD HEC E 301 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC E 301 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC E 301 " -0.005 2.00e-02 2.50e+03 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 151 2.51 - 3.11: 7222 3.11 - 3.71: 14154 3.71 - 4.30: 19683 4.30 - 4.90: 30611 Nonbonded interactions: 71821 Sorted by model distance: nonbonded pdb=" ND2 ASN A 197 " pdb=" ND2 ASN D 207 " model vdw 1.918 3.200 nonbonded pdb=" ND2 ASN B 197 " pdb=" ND2 ASN C 207 " model vdw 1.918 3.200 nonbonded pdb=" ND2 ASN D 197 " pdb=" ND2 ASN E 207 " model vdw 1.918 3.200 nonbonded pdb=" ND2 ASN A 207 " pdb=" ND2 ASN C 197 " model vdw 1.918 3.200 nonbonded pdb=" CD1 ILE D 37 " pdb=" O1A HEC E 303 " model vdw 2.016 3.460 ... (remaining 71816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.490 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.230 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 43.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.006 0.099 9415 Z= 0.423 Angle : 1.052 13.382 13145 Z= 0.580 Chirality : 0.097 1.210 1265 Planarity : 0.005 0.035 1655 Dihedral : 17.242 83.879 2965 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 47.42 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.63 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 1.02 % 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: -2.33 (0.25), residues: 1090 helix: 1.43 (0.42), residues: 145 sheet: -0.69 (0.50), residues: 100 loop : -2.43 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 34 HIS 0.006 0.001 HIS E 189 PHE 0.006 0.002 PHE D 239 TYR 0.015 0.002 TYR B 223 ARG 0.001 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7276 (tp30) cc_final: 0.6110 (mm-30) REVERT: C 59 ASN cc_start: 0.8837 (t0) cc_final: 0.8261 (t0) REVERT: C 65 LYS cc_start: 0.8241 (ptpt) cc_final: 0.7998 (ptpt) REVERT: D 65 LYS cc_start: 0.8297 (ptpt) cc_final: 0.8025 (ptpt) REVERT: E 65 LYS cc_start: 0.8267 (ptpt) cc_final: 0.8059 (ptpt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2271 time to fit residues: 44.8983 Evaluate side-chains 107 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 HIS ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 HIS E 64 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 9415 Z= 0.390 Angle : 0.961 15.765 13145 Z= 0.372 Chirality : 0.042 0.122 1265 Planarity : 0.003 0.025 1655 Dihedral : 15.419 87.917 1325 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.08 % Favored : 90.46 % Rotamer: Outliers : 2.07 % Allowed : 11.15 % Favored : 86.78 % 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: -2.34 (0.25), residues: 1090 helix: 0.75 (0.40), residues: 145 sheet: -1.80 (0.43), residues: 120 loop : -2.13 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 198 HIS 0.008 0.001 HIS A 64 PHE 0.016 0.002 PHE D 239 TYR 0.017 0.002 TYR A 223 ARG 0.003 0.001 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.950 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 65 LYS cc_start: 0.8041 (pttt) cc_final: 0.7841 (ptpt) REVERT: B 163 GLU cc_start: 0.7336 (tp30) cc_final: 0.6352 (mm-30) REVERT: C 59 ASN cc_start: 0.8782 (t0) cc_final: 0.7940 (t0) REVERT: C 65 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7770 (ptpt) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.1961 time to fit residues: 37.2599 Evaluate side-chains 126 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 200 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN C 43 ASN C 60 ASN D 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9415 Z= 0.196 Angle : 0.777 10.813 13145 Z= 0.305 Chirality : 0.039 0.117 1265 Planarity : 0.002 0.018 1655 Dihedral : 15.017 87.711 1325 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.33 % Favored : 93.21 % Rotamer: Outliers : 2.07 % Allowed : 14.83 % Favored : 83.10 % 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: -2.22 (0.26), residues: 1090 helix: 0.67 (0.42), residues: 145 sheet: -1.79 (0.43), residues: 120 loop : -1.99 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 198 HIS 0.002 0.000 HIS C 32 PHE 0.011 0.001 PHE D 138 TYR 0.013 0.001 TYR A 223 ARG 0.002 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.993 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: B 163 GLU cc_start: 0.7290 (tp30) cc_final: 0.6227 (mm-30) REVERT: C 65 LYS cc_start: 0.8023 (ptpt) cc_final: 0.7769 (ptpt) REVERT: D 65 LYS cc_start: 0.8332 (ptpt) cc_final: 0.8090 (mttt) outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 0.1927 time to fit residues: 36.6206 Evaluate side-chains 128 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 200 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 9415 Z= 0.380 Angle : 0.941 17.145 13145 Z= 0.348 Chirality : 0.041 0.121 1265 Planarity : 0.003 0.024 1655 Dihedral : 15.309 88.727 1325 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.72 % Favored : 90.83 % Rotamer: Outliers : 3.33 % Allowed : 18.39 % Favored : 78.28 % 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: -2.31 (0.26), residues: 1090 helix: 0.53 (0.40), residues: 145 sheet: -1.80 (0.38), residues: 145 loop : -2.04 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 34 HIS 0.004 0.001 HIS A 32 PHE 0.015 0.002 PHE C 239 TYR 0.014 0.001 TYR E 152 ARG 0.002 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.953 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7344 (tp30) cc_final: 0.6568 (mm-30) REVERT: C 65 LYS cc_start: 0.7977 (ptpt) cc_final: 0.7765 (ptpt) REVERT: D 216 THR cc_start: 0.2111 (OUTLIER) cc_final: 0.1899 (p) outliers start: 29 outliers final: 22 residues processed: 140 average time/residue: 0.1846 time to fit residues: 37.0867 Evaluate side-chains 124 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 200 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9415 Z= 0.340 Angle : 0.910 16.508 13145 Z= 0.340 Chirality : 0.040 0.123 1265 Planarity : 0.003 0.025 1655 Dihedral : 15.326 89.861 1325 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.06 % Favored : 92.48 % Rotamer: Outliers : 4.48 % Allowed : 20.23 % Favored : 75.29 % 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: -2.36 (0.26), residues: 1090 helix: 0.51 (0.40), residues: 145 sheet: -1.89 (0.38), residues: 145 loop : -2.05 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 HIS 0.005 0.001 HIS E 32 PHE 0.017 0.002 PHE B 54 TYR 0.019 0.001 TYR B 152 ARG 0.001 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 108 time to evaluate : 0.948 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7820 (ptpt) REVERT: B 76 HIS cc_start: 0.8508 (m170) cc_final: 0.8081 (m170) REVERT: B 163 GLU cc_start: 0.7301 (tp30) cc_final: 0.6571 (mm-30) REVERT: C 65 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7877 (ptpt) REVERT: D 65 LYS cc_start: 0.8163 (ptpt) cc_final: 0.7959 (mttt) REVERT: E 76 HIS cc_start: 0.8375 (m170) cc_final: 0.7815 (m-70) outliers start: 39 outliers final: 26 residues processed: 140 average time/residue: 0.1846 time to fit residues: 37.3389 Evaluate side-chains 132 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 9415 Z= 0.367 Angle : 0.945 17.888 13145 Z= 0.351 Chirality : 0.041 0.211 1265 Planarity : 0.003 0.026 1655 Dihedral : 15.407 88.935 1325 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.82 % Favored : 89.72 % Rotamer: Outliers : 4.48 % Allowed : 21.61 % Favored : 73.91 % 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: -2.40 (0.26), residues: 1090 helix: 0.40 (0.39), residues: 145 sheet: -1.96 (0.37), residues: 145 loop : -2.06 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 34 HIS 0.004 0.001 HIS E 108 PHE 0.021 0.002 PHE D 54 TYR 0.019 0.002 TYR D 152 ARG 0.002 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 112 time to evaluate : 0.861 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 HIS cc_start: 0.8454 (m170) cc_final: 0.7924 (m-70) REVERT: B 163 GLU cc_start: 0.7131 (tp30) cc_final: 0.6596 (mm-30) REVERT: C 65 LYS cc_start: 0.8053 (ptpt) cc_final: 0.7791 (ptpt) REVERT: E 32 HIS cc_start: 0.3433 (OUTLIER) cc_final: 0.2423 (m90) REVERT: E 65 LYS cc_start: 0.7549 (mttt) cc_final: 0.7278 (mttt) REVERT: E 76 HIS cc_start: 0.8420 (m170) cc_final: 0.7832 (m-70) REVERT: E 170 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8606 (mt-10) outliers start: 39 outliers final: 27 residues processed: 145 average time/residue: 0.1888 time to fit residues: 39.2353 Evaluate side-chains 132 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 247 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 9415 Z= 0.532 Angle : 1.089 21.749 13145 Z= 0.413 Chirality : 0.045 0.209 1265 Planarity : 0.004 0.030 1655 Dihedral : 15.619 87.870 1325 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 25.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.73 % Favored : 88.90 % Rotamer: Outliers : 6.44 % Allowed : 20.80 % Favored : 72.76 % 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: -2.75 (0.25), residues: 1090 helix: -0.03 (0.37), residues: 145 sheet: -2.23 (0.36), residues: 145 loop : -2.27 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 34 HIS 0.007 0.001 HIS E 32 PHE 0.031 0.003 PHE E 54 TYR 0.023 0.002 TYR A 152 ARG 0.006 0.001 ARG E 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 104 time to evaluate : 0.923 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 HIS cc_start: 0.8637 (m170) cc_final: 0.8141 (m-70) REVERT: B 163 GLU cc_start: 0.7210 (tp30) cc_final: 0.6914 (mm-30) REVERT: C 65 LYS cc_start: 0.7998 (ptpt) cc_final: 0.7724 (ptpt) REVERT: D 60 ASN cc_start: 0.8809 (t0) cc_final: 0.8524 (t0) REVERT: D 76 HIS cc_start: 0.8303 (m170) cc_final: 0.7849 (m-70) REVERT: E 48 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8044 (mtpp) REVERT: E 65 LYS cc_start: 0.7592 (mttt) cc_final: 0.7305 (mttt) REVERT: E 76 HIS cc_start: 0.8465 (m170) cc_final: 0.7931 (m-70) outliers start: 56 outliers final: 39 residues processed: 149 average time/residue: 0.1823 time to fit residues: 39.4164 Evaluate side-chains 138 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.0050 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 0.0670 overall best weight: 0.4932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9415 Z= 0.218 Angle : 0.854 13.649 13145 Z= 0.328 Chirality : 0.040 0.140 1265 Planarity : 0.003 0.025 1655 Dihedral : 15.178 89.517 1325 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.61 % Favored : 92.02 % Rotamer: Outliers : 4.14 % Allowed : 22.64 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.26), residues: 1090 helix: 0.03 (0.40), residues: 145 sheet: -2.02 (0.42), residues: 120 loop : -2.10 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 34 HIS 0.005 0.001 HIS E 50 PHE 0.026 0.002 PHE B 138 TYR 0.014 0.001 TYR B 152 ARG 0.002 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 0.863 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: symmetry clash REVERT: B 76 HIS cc_start: 0.8347 (m170) cc_final: 0.8013 (m-70) REVERT: C 65 LYS cc_start: 0.8017 (ptpt) cc_final: 0.7716 (ptpt) REVERT: D 60 ASN cc_start: 0.8730 (t0) cc_final: 0.8290 (t0) REVERT: D 76 HIS cc_start: 0.8026 (m170) cc_final: 0.7545 (m-70) REVERT: E 48 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7006 (ttmm) REVERT: E 76 HIS cc_start: 0.8098 (m170) cc_final: 0.7684 (m-70) REVERT: E 221 THR cc_start: 0.8152 (p) cc_final: 0.7927 (t) outliers start: 36 outliers final: 26 residues processed: 147 average time/residue: 0.1761 time to fit residues: 38.1966 Evaluate side-chains 135 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7671 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9415 Z= 0.283 Angle : 0.929 19.299 13145 Z= 0.338 Chirality : 0.041 0.225 1265 Planarity : 0.003 0.021 1655 Dihedral : 15.087 88.263 1325 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.08 % Favored : 90.55 % Rotamer: Outliers : 4.60 % Allowed : 23.91 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.26), residues: 1090 helix: 0.08 (0.40), residues: 145 sheet: -1.93 (0.42), residues: 120 loop : -2.09 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 34 HIS 0.004 0.001 HIS A 189 PHE 0.022 0.002 PHE C 54 TYR 0.023 0.001 TYR D 152 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 111 time to evaluate : 0.895 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.8839 (ptpt) cc_final: 0.8482 (ptpt) REVERT: B 72 ASP cc_start: 0.8852 (p0) cc_final: 0.8442 (p0) REVERT: C 65 LYS cc_start: 0.8040 (ptpt) cc_final: 0.7746 (ptpt) REVERT: D 60 ASN cc_start: 0.8670 (t0) cc_final: 0.8401 (t0) REVERT: E 76 HIS cc_start: 0.8262 (m170) cc_final: 0.7796 (m-70) REVERT: E 221 THR cc_start: 0.8192 (p) cc_final: 0.7930 (t) outliers start: 40 outliers final: 31 residues processed: 144 average time/residue: 0.1795 time to fit residues: 37.6682 Evaluate side-chains 139 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.2980 chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 0.0670 chunk 87 optimal weight: 8.9990 chunk 9 optimal weight: 0.0670 chunk 67 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- 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: 0.7553 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9415 Z= 0.200 Angle : 0.839 16.398 13145 Z= 0.318 Chirality : 0.039 0.146 1265 Planarity : 0.003 0.020 1655 Dihedral : 14.838 86.650 1325 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.71 % Favored : 91.93 % Rotamer: Outliers : 3.45 % Allowed : 24.94 % Favored : 71.61 % 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: -2.47 (0.25), residues: 1090 helix: 0.15 (0.41), residues: 145 sheet: -1.67 (0.44), residues: 120 loop : -2.14 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 34 HIS 0.003 0.001 HIS A 189 PHE 0.019 0.002 PHE E 138 TYR 0.013 0.001 TYR A 152 ARG 0.005 0.000 ARG C 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 0.923 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.8825 (ptpt) cc_final: 0.8468 (ptpt) REVERT: B 72 ASP cc_start: 0.8837 (p0) cc_final: 0.8431 (p0) REVERT: C 65 LYS cc_start: 0.8076 (ptpt) cc_final: 0.7780 (ptpt) REVERT: D 60 ASN cc_start: 0.8533 (t0) cc_final: 0.8266 (t0) REVERT: E 76 HIS cc_start: 0.8099 (m170) cc_final: 0.7722 (m170) REVERT: E 221 THR cc_start: 0.8034 (p) cc_final: 0.7799 (t) outliers start: 30 outliers final: 27 residues processed: 147 average time/residue: 0.1650 time to fit residues: 35.6919 Evaluate side-chains 139 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.095814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077548 restraints weight = 28564.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080251 restraints weight = 16167.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.082070 restraints weight = 11385.782| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9415 Z= 0.315 Angle : 0.988 24.322 13145 Z= 0.346 Chirality : 0.041 0.196 1265 Planarity : 0.003 0.020 1655 Dihedral : 14.892 87.766 1325 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.45 % Favored : 90.18 % Rotamer: Outliers : 3.91 % Allowed : 25.40 % Favored : 70.69 % 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 (0.26), residues: 1090 helix: 0.25 (0.40), residues: 145 sheet: -1.64 (0.44), residues: 120 loop : -2.14 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 34 HIS 0.011 0.001 HIS A 189 PHE 0.031 0.002 PHE E 138 TYR 0.014 0.001 TYR C 210 ARG 0.002 0.000 ARG D 78 =============================================================================== Job complete usr+sys time: 1832.68 seconds wall clock time: 33 minutes 58.73 seconds (2038.73 seconds total)