Starting phenix.real_space_refine on Fri Jul 3 20:34:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyk_18756/07_2026/8qyk_18756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyk_18756/07_2026/8qyk_18756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qyk_18756/07_2026/8qyk_18756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyk_18756/07_2026/8qyk_18756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qyk_18756/07_2026/8qyk_18756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyk_18756/07_2026/8qyk_18756.map" } resolution = 2.07 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.095 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 49 5.16 5 C 9997 2.51 5 N 2417 2.21 5 O 3699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16182 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2129 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Conformer: "B" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} bond proxies already assigned to first conformer: 2158 Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "C" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 255} Chain: "D" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "E" Number of atoms: 2127 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Conformer: "B" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} bond proxies already assigned to first conformer: 2160 Chain: "F" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "G" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "D" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 163 Classifications: {'water': 163} Link IDs: {None: 162} Chain: "E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 170 Classifications: {'water': 170} Link IDs: {None: 169} Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 4.21, per 1000 atoms: 0.26 Number of scatterers: 16182 At special positions: 0 Unit cell: (84.032, 82.368, 227.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 49 16.00 P 15 15.00 O 3699 8.00 N 2417 7.00 C 9997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 86 " distance=2.03 Simple disulfide: pdb=" SG CYS F 165 " - pdb=" SG CYS F 240 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 86 " distance=2.03 Simple disulfide: pdb=" SG CYS G 165 " - pdb=" SG CYS G 240 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.69 Conformation dependent library (CDL) restraints added in 908.8 milliseconds 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3476 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 7 sheets defined 78.3% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 17 through 38 Processing helix chain 'A' and resid 38 through 58 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 134 through 158 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 165 through 218 Processing helix chain 'A' and resid 223 through 265 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 13 through 14 No H-bonds generated for 'chain 'B' and resid 13 through 14' Processing helix chain 'B' and resid 15 through 16 No H-bonds generated for 'chain 'B' and resid 15 through 16' Processing helix chain 'B' and resid 17 through 38 Processing helix chain 'B' and resid 38 through 58 Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 134 through 158 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 165 through 218 Processing helix chain 'B' and resid 223 through 265 removed outlier: 3.566A pdb=" N GLU B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 14 through 16 No H-bonds generated for 'chain 'C' and resid 14 through 16' Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 38 through 59 Processing helix chain 'C' and resid 63 through 75 Processing helix chain 'C' and resid 77 through 90 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 162 through 220 removed outlier: 3.723A pdb=" N LEU C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 265 removed outlier: 3.544A pdb=" N GLU C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 17 through 38 removed outlier: 3.504A pdb=" N VAL D 21 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 58 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.485A pdb=" N ARG D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 134 through 158 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 165 through 220 removed outlier: 3.805A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 265 removed outlier: 3.582A pdb=" N GLU D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 17 through 38 Processing helix chain 'E' and resid 38 through 58 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 77 through 90 Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 134 through 157 Processing helix chain 'E' and resid 162 through 218 Processing helix chain 'E' and resid 223 through 265 Processing helix chain 'F' and resid 19 through 79 Processing helix chain 'F' and resid 107 through 127 removed outlier: 3.736A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 148 through 169 Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.876A pdb=" N LYS F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 203 through 208 removed outlier: 3.514A pdb=" N ARG F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 47 removed outlier: 3.976A pdb=" N ILE G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 79 Processing helix chain 'G' and resid 107 through 127 Proline residue: G 119 - end of helix removed outlier: 3.517A pdb=" N SER G 127 " --> pdb=" O GLU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 133 Processing helix chain 'G' and resid 148 through 168 removed outlier: 3.541A pdb=" N ASN G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 177 removed outlier: 3.618A pdb=" N LYS G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN G 177 " --> pdb=" O PRO G 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 177' Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'G' and resid 203 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 98 removed outlier: 3.631A pdb=" N ARG A 106 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 96 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE A 104 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU A 98 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 98 removed outlier: 3.698A pdb=" N ARG B 106 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU B 96 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE B 104 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU B 98 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 97 removed outlier: 3.689A pdb=" N ARG C 106 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU C 96 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 104 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 98 removed outlier: 3.766A pdb=" N ARG D 106 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU D 96 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE D 104 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU D 98 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 98 removed outlier: 3.690A pdb=" N ARG E 106 " --> pdb=" O GLN E 94 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU E 96 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE E 104 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLU E 98 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 82 through 85 removed outlier: 5.025A pdb=" N PHE F 93 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL F 210 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLU F 211 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE F 139 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG F 213 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE F 137 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLN F 215 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER F 196 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY F 141 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 83 through 85 removed outlier: 3.537A pdb=" N VAL G 83 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU G 211 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN G 215 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN G 136 " --> pdb=" O GLN G 215 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N LEU G 191 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE G 137 " --> pdb=" O LEU G 191 " (cutoff:3.500A) 1126 hydrogen bonds defined for protein. 3327 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: 2.75 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2406 1.28 - 1.41: 3760 1.41 - 1.54: 9147 1.54 - 1.68: 201 1.68 - 1.81: 95 Bond restraints: 15609 Sorted by residual: bond pdb=" C38 PEE B 502 " pdb=" C39 PEE B 502 " ideal model delta sigma weight residual 1.523 1.353 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C38 PEE E 502 " pdb=" C39 PEE E 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" C38 PEE C 502 " pdb=" C39 PEE C 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C38 PEE A 502 " pdb=" C39 PEE A 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" C38 PEE D 502 " pdb=" C39 PEE D 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.11e+01 ... (remaining 15604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.41: 20903 10.41 - 20.82: 19 20.82 - 31.23: 0 31.23 - 41.65: 0 41.65 - 52.06: 10 Bond angle restraints: 20932 Sorted by residual: angle pdb=" C38 PEE D 502 " pdb=" C39 PEE D 502 " pdb=" C40 PEE D 502 " ideal model delta sigma weight residual 112.47 164.53 -52.06 3.00e+00 1.11e-01 3.01e+02 angle pdb=" C38 PEE A 502 " pdb=" C39 PEE A 502 " pdb=" C40 PEE A 502 " ideal model delta sigma weight residual 112.47 164.23 -51.76 3.00e+00 1.11e-01 2.98e+02 angle pdb=" C38 PEE E 502 " pdb=" C39 PEE E 502 " pdb=" C40 PEE E 502 " ideal model delta sigma weight residual 112.47 164.05 -51.58 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C38 PEE B 502 " pdb=" C39 PEE B 502 " pdb=" C40 PEE B 502 " ideal model delta sigma weight residual 112.47 163.83 -51.36 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C38 PEE C 502 " pdb=" C39 PEE C 502 " pdb=" C40 PEE C 502 " ideal model delta sigma weight residual 112.47 163.55 -51.08 3.00e+00 1.11e-01 2.90e+02 ... (remaining 20927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 9149 32.97 - 65.94: 502 65.94 - 98.90: 35 98.90 - 131.87: 19 131.87 - 164.84: 12 Dihedral angle restraints: 9717 sinusoidal: 4366 harmonic: 5351 Sorted by residual: dihedral pdb=" CD ARG F 52 " pdb=" NE ARG F 52 " pdb=" CZ ARG F 52 " pdb=" NH1 ARG F 52 " ideal model delta sinusoidal sigma weight residual 0.00 -72.81 72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" C3 PEE D 502 " pdb=" C1 PEE D 502 " pdb=" C2 PEE D 502 " pdb=" O3P PEE D 502 " ideal model delta sinusoidal sigma weight residual 62.73 -102.11 164.84 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C3 PEE B 502 " pdb=" C1 PEE B 502 " pdb=" C2 PEE B 502 " pdb=" O3P PEE B 502 " ideal model delta sinusoidal sigma weight residual 62.73 -99.08 161.81 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 9714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2267 0.111 - 0.221: 32 0.221 - 0.332: 1 0.332 - 0.442: 1 0.442 - 0.553: 5 Chirality restraints: 2306 Sorted by residual: chirality pdb=" C2 PEE E 502 " pdb=" C1 PEE E 502 " pdb=" C3 PEE E 502 " pdb=" O2 PEE E 502 " both_signs ideal model delta sigma weight residual False -2.33 -2.88 0.55 2.00e-01 2.50e+01 7.64e+00 chirality pdb=" C2 PEE B 502 " pdb=" C1 PEE B 502 " pdb=" C3 PEE B 502 " pdb=" O2 PEE B 502 " both_signs ideal model delta sigma weight residual False -2.33 -2.88 0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" C2 PEE D 502 " pdb=" C1 PEE D 502 " pdb=" C3 PEE D 502 " pdb=" O2 PEE D 502 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.55 2.00e-01 2.50e+01 7.48e+00 ... (remaining 2303 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 52 " -1.028 9.50e-02 1.11e+02 4.61e-01 1.28e+02 pdb=" NE ARG F 52 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG F 52 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 52 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 52 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 12 " -0.676 9.50e-02 1.11e+02 3.03e-01 5.59e+01 pdb=" NE ARG G 12 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG G 12 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 12 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 12 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 49 " -0.239 9.50e-02 1.11e+02 1.07e-01 7.22e+00 pdb=" NE ARG F 49 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG F 49 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 49 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 49 " -0.006 2.00e-02 2.50e+03 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 565 2.68 - 3.23: 15728 3.23 - 3.79: 28914 3.79 - 4.34: 37400 4.34 - 4.90: 60121 Nonbonded interactions: 142728 Sorted by model distance: nonbonded pdb=" O HOH E 642 " pdb=" O HOH E 669 " model vdw 2.122 3.040 nonbonded pdb=" O HOH D 610 " pdb=" O HOH D 744 " model vdw 2.137 3.040 nonbonded pdb=" O LYS G 18 " pdb=" O HOH G 301 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASN B 5 " pdb=" NH2 ARG C 175 " model vdw 2.159 3.120 nonbonded pdb=" OH TYR E 208 " pdb=" OA4 CDL E 501 " model vdw 2.166 3.040 ... (remaining 142723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 503)) selection = (chain 'B' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 503)) selection = (chain 'C' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 503)) selection = (chain 'D' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 503)) selection = (chain 'E' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 503)) } ncs_group { reference = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 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:5.820 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.009 0.170 15613 Z= 0.454 Angle : 1.408 52.057 20940 Z= 0.540 Chirality : 0.048 0.553 2306 Planarity : 0.012 0.461 2566 Dihedral : 20.116 164.839 6229 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.19 % Allowed : 0.25 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.20), residues: 1807 helix: 3.39 (0.13), residues: 1266 sheet: -0.97 (0.89), residues: 36 loop : -0.27 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 52 TYR 0.023 0.002 TYR E 208 PHE 0.021 0.002 PHE A 181 TRP 0.018 0.002 TRP A 84 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00894 / 0.45 (15609) covalent geometry : angle 1.40817 / 0.54 (20932) SS BOND : bond 0.00111 / 0.06 ( 4) SS BOND : angle 0.79722 / 0.34 ( 8) hydrogen bonds : bond 0.10687 / 6.89 ( 1126) hydrogen bonds : angle 4.52773 / 3.24 ( 3327) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8841 (m-80) cc_final: 0.8598 (m-80) REVERT: B 5 ASN cc_start: 0.7260 (m-40) cc_final: 0.6884 (m110) REVERT: B 69 GLU cc_start: 0.7503 (pp20) cc_final: 0.7273 (pp20) REVERT: B 102 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6310 (mm-30) REVERT: B 152 MET cc_start: 0.9125 (mtm) cc_final: 0.8872 (mtp) REVERT: C 11 LEU cc_start: 0.8503 (mt) cc_final: 0.8289 (mt) REVERT: F 244 MET cc_start: 0.1672 (ptp) cc_final: 0.1453 (pmm) REVERT: G 11 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.5495 (ptp-170) REVERT: G 164 MET cc_start: 0.3067 (ttm) cc_final: 0.2372 (ttt) REVERT: G 244 MET cc_start: 0.0484 (mtt) cc_final: 0.0216 (tpp) outliers start: 3 outliers final: 0 residues processed: 181 average time/residue: 0.6866 time to fit residues: 134.7061 Evaluate side-chains 146 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN B 134 HIS B 157 HIS C 121 GLN D 165 GLN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.210036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125291 restraints weight = 20066.825| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.98 r_work: 0.3279 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15613 Z= 0.144 Angle : 0.528 7.669 20940 Z= 0.273 Chirality : 0.039 0.163 2306 Planarity : 0.004 0.050 2566 Dihedral : 20.536 177.104 2739 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.68 % Allowed : 4.95 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.20), residues: 1807 helix: 3.59 (0.13), residues: 1260 sheet: -1.29 (0.84), residues: 36 loop : -0.15 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 77 TYR 0.019 0.002 TYR B 208 PHE 0.017 0.002 PHE A 181 TRP 0.018 0.001 TRP D 84 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (15609) covalent geometry : angle 0.52779 / 0.27 (20932) SS BOND : bond 0.00114 / 0.06 ( 4) SS BOND : angle 0.73921 / 0.36 ( 8) hydrogen bonds : bond 0.05325 / 3.47 ( 1126) hydrogen bonds : angle 3.92841 / 2.81 ( 3327) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8914 (m-80) cc_final: 0.8661 (m-80) REVERT: A 257 MET cc_start: 0.3334 (mtp) cc_final: 0.3075 (ttt) REVERT: B 44 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8105 (ttp-170) REVERT: B 69 GLU cc_start: 0.7754 (pp20) cc_final: 0.7448 (pp20) REVERT: B 102 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6876 (mm-30) REVERT: B 152 MET cc_start: 0.9102 (mtm) cc_final: 0.8887 (mtp) REVERT: C 11 LEU cc_start: 0.8616 (mt) cc_final: 0.8382 (mt) REVERT: C 61 LYS cc_start: 0.8484 (mmtm) cc_final: 0.8178 (mptt) REVERT: D 130 GLU cc_start: 0.8176 (mp0) cc_final: 0.7289 (pm20) REVERT: D 257 MET cc_start: 0.3211 (tmm) cc_final: 0.2158 (mtp) REVERT: E 65 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: E 72 LYS cc_start: 0.8420 (tptt) cc_final: 0.8129 (tttp) REVERT: F 4 ASN cc_start: 0.6308 (p0) cc_final: 0.5966 (t0) REVERT: F 244 MET cc_start: 0.1433 (ptp) cc_final: 0.1206 (pmm) REVERT: G 11 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5388 (ptp90) REVERT: G 51 GLN cc_start: 0.7014 (mt0) cc_final: 0.6626 (mt0) REVERT: G 164 MET cc_start: 0.2818 (ttm) cc_final: 0.2260 (ttp) REVERT: G 244 MET cc_start: 0.0365 (mtt) cc_final: 0.0147 (tpp) outliers start: 11 outliers final: 5 residues processed: 160 average time/residue: 0.6543 time to fit residues: 113.9666 Evaluate side-chains 150 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain G residue 11 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 160 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN B 165 GLN C 121 GLN E 171 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.206028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121858 restraints weight = 17805.118| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.44 r_work: 0.3242 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15613 Z= 0.204 Angle : 0.602 9.000 20940 Z= 0.312 Chirality : 0.043 0.166 2306 Planarity : 0.005 0.056 2566 Dihedral : 19.507 179.111 2739 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.74 % Allowed : 6.62 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.19), residues: 1807 helix: 3.30 (0.13), residues: 1266 sheet: -1.14 (0.74), residues: 46 loop : -0.15 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 44 TYR 0.028 0.002 TYR B 208 PHE 0.027 0.002 PHE A 181 TRP 0.022 0.002 TRP B 84 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (15609) covalent geometry : angle 0.60238 / 0.31 (20932) SS BOND : bond 0.00145 / 0.07 ( 4) SS BOND : angle 0.78971 / 0.42 ( 8) hydrogen bonds : bond 0.06045 / 3.91 ( 1126) hydrogen bonds : angle 4.09268 / 2.93 ( 3327) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3302 (mtp) cc_final: 0.3094 (ttt) REVERT: B 61 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8612 (mtpt) REVERT: B 69 GLU cc_start: 0.7618 (pp20) cc_final: 0.7293 (pp20) REVERT: B 102 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7257 (mm-30) REVERT: B 152 MET cc_start: 0.9075 (mtm) cc_final: 0.8797 (mtp) REVERT: B 167 SER cc_start: 0.8733 (m) cc_final: 0.8435 (t) REVERT: C 61 LYS cc_start: 0.8463 (mmtm) cc_final: 0.8215 (mptt) REVERT: E 65 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: E 72 LYS cc_start: 0.8423 (tptt) cc_final: 0.8142 (tttp) REVERT: F 1 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.4782 (ttt) REVERT: F 153 LEU cc_start: 0.2642 (tp) cc_final: 0.2093 (mm) REVERT: G 11 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.6035 (ptp90) REVERT: G 51 GLN cc_start: 0.6939 (mt0) cc_final: 0.6335 (mt0) REVERT: G 164 MET cc_start: 0.2866 (ttm) cc_final: 0.2326 (ttp) REVERT: G 244 MET cc_start: 0.0518 (mtt) cc_final: 0.0280 (tpp) outliers start: 12 outliers final: 4 residues processed: 170 average time/residue: 0.6565 time to fit residues: 121.5840 Evaluate side-chains 153 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 11 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 95 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 121 GLN B 165 GLN C 121 GLN E 171 ASN F 241 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.208241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124747 restraints weight = 29479.119| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.95 r_work: 0.3210 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15613 Z= 0.135 Angle : 0.500 7.918 20940 Z= 0.261 Chirality : 0.038 0.210 2306 Planarity : 0.004 0.057 2566 Dihedral : 18.494 178.851 2739 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.11 % Allowed : 7.54 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.20), residues: 1807 helix: 3.54 (0.13), residues: 1264 sheet: -1.07 (0.73), residues: 46 loop : -0.03 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 223 TYR 0.018 0.001 TYR B 208 PHE 0.015 0.001 PHE A 181 TRP 0.019 0.002 TRP D 84 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (15609) covalent geometry : angle 0.49982 / 0.26 (20932) SS BOND : bond 0.00149 / 0.07 ( 4) SS BOND : angle 0.54717 / 0.30 ( 8) hydrogen bonds : bond 0.05113 / 3.34 ( 1126) hydrogen bonds : angle 3.80836 / 2.74 ( 3327) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3316 (mtp) cc_final: 0.2966 (ttt) REVERT: B 44 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7978 (ttp-170) REVERT: B 61 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8567 (mtpt) REVERT: B 69 GLU cc_start: 0.7596 (pp20) cc_final: 0.7282 (pp20) REVERT: B 152 MET cc_start: 0.8988 (mtm) cc_final: 0.8709 (mtp) REVERT: C 61 LYS cc_start: 0.8385 (mmtm) cc_final: 0.8100 (mptt) REVERT: D 130 GLU cc_start: 0.8049 (mp0) cc_final: 0.7198 (pm20) REVERT: D 257 MET cc_start: 0.3164 (OUTLIER) cc_final: 0.1911 (mtp) REVERT: E 65 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: E 72 LYS cc_start: 0.8305 (tptt) cc_final: 0.8022 (tttp) REVERT: F 1 MET cc_start: 0.5370 (OUTLIER) cc_final: 0.4626 (ttt) REVERT: F 122 LEU cc_start: 0.2381 (mm) cc_final: 0.2115 (pp) REVERT: G 164 MET cc_start: 0.2405 (ttm) cc_final: 0.1913 (ttp) REVERT: G 244 MET cc_start: 0.0457 (mtt) cc_final: 0.0230 (tpp) outliers start: 18 outliers final: 5 residues processed: 167 average time/residue: 0.6537 time to fit residues: 119.4681 Evaluate side-chains 158 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 122 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 147 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 121 GLN B 165 GLN C 76 GLN C 121 GLN E 171 ASN F 87 HIS G 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.207626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124260 restraints weight = 22740.017| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.30 r_work: 0.3241 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15613 Z= 0.144 Angle : 0.516 9.434 20940 Z= 0.269 Chirality : 0.039 0.223 2306 Planarity : 0.004 0.056 2566 Dihedral : 17.948 177.745 2735 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.11 % Allowed : 8.47 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.73 (0.19), residues: 1807 helix: 3.49 (0.13), residues: 1269 sheet: -1.03 (0.73), residues: 46 loop : -0.08 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 11 TYR 0.021 0.002 TYR B 208 PHE 0.019 0.002 PHE A 181 TRP 0.018 0.002 TRP B 84 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (15609) covalent geometry : angle 0.51587 / 0.27 (20932) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 0.57742 / 0.33 ( 8) hydrogen bonds : bond 0.05247 / 3.41 ( 1126) hydrogen bonds : angle 3.83220 / 2.75 ( 3327) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7599 (tmtm) REVERT: B 44 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8581 (mtp180) REVERT: B 61 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8635 (mtpt) REVERT: B 77 ARG cc_start: 0.6271 (tmm-80) cc_final: 0.5762 (ttt180) REVERT: B 152 MET cc_start: 0.9046 (mtm) cc_final: 0.8776 (mtp) REVERT: C 61 LYS cc_start: 0.8437 (mmtm) cc_final: 0.8111 (mptt) REVERT: D 11 LEU cc_start: 0.7649 (mt) cc_final: 0.7388 (mp) REVERT: D 130 GLU cc_start: 0.8206 (mp0) cc_final: 0.7298 (pm20) REVERT: E 65 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: E 72 LYS cc_start: 0.8401 (tptt) cc_final: 0.8091 (tttp) REVERT: F 1 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.4635 (ttt) REVERT: F 4 ASN cc_start: 0.6351 (p0) cc_final: 0.5992 (t0) REVERT: F 153 LEU cc_start: 0.3119 (OUTLIER) cc_final: 0.2895 (pp) REVERT: G 164 MET cc_start: 0.2246 (ttm) cc_final: 0.1850 (ttp) REVERT: G 214 MET cc_start: 0.1531 (pmm) cc_final: 0.1023 (ttp) REVERT: G 244 MET cc_start: 0.0407 (mtt) cc_final: -0.0319 (tpp) outliers start: 18 outliers final: 6 residues processed: 159 average time/residue: 0.6176 time to fit residues: 107.7171 Evaluate side-chains 158 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 145 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 12 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 121 GLN B 165 GLN C 76 GLN C 121 GLN D 121 GLN E 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.208801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122551 restraints weight = 27050.016| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.56 r_work: 0.3220 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15613 Z= 0.137 Angle : 0.502 8.886 20940 Z= 0.263 Chirality : 0.038 0.234 2306 Planarity : 0.004 0.055 2566 Dihedral : 17.392 178.572 2735 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.11 % Allowed : 8.60 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.84 (0.19), residues: 1807 helix: 3.59 (0.13), residues: 1264 sheet: -1.05 (0.71), residues: 46 loop : -0.02 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 223 TYR 0.022 0.001 TYR B 208 PHE 0.017 0.001 PHE A 181 TRP 0.018 0.002 TRP D 84 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (15609) covalent geometry : angle 0.50199 / 0.26 (20932) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 0.57303 / 0.32 ( 8) hydrogen bonds : bond 0.05091 / 3.32 ( 1126) hydrogen bonds : angle 3.76114 / 2.71 ( 3327) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8257 (mt) cc_final: 0.7916 (mp) REVERT: A 72 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7528 (tmtm) REVERT: B 44 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8539 (mtp180) REVERT: B 61 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8622 (mtpt) REVERT: B 69 GLU cc_start: 0.7479 (pp20) cc_final: 0.7252 (pp20) REVERT: B 77 ARG cc_start: 0.6251 (tmm-80) cc_final: 0.5741 (ttt180) REVERT: B 152 MET cc_start: 0.9000 (mtm) cc_final: 0.8749 (mtp) REVERT: C 61 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8033 (mptt) REVERT: D 11 LEU cc_start: 0.7536 (mt) cc_final: 0.7262 (mp) REVERT: D 130 GLU cc_start: 0.8140 (mp0) cc_final: 0.7186 (pm20) REVERT: E 65 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: E 72 LYS cc_start: 0.8326 (tptt) cc_final: 0.7996 (tttp) REVERT: F 1 MET cc_start: 0.5224 (OUTLIER) cc_final: 0.4202 (ttt) REVERT: F 4 ASN cc_start: 0.6310 (p0) cc_final: 0.5919 (t0) REVERT: G 51 GLN cc_start: 0.6636 (mt0) cc_final: 0.5932 (mt0) REVERT: G 164 MET cc_start: 0.2411 (ttm) cc_final: 0.2071 (ttp) REVERT: G 244 MET cc_start: 0.0075 (mtt) cc_final: -0.0512 (tpp) outliers start: 18 outliers final: 6 residues processed: 163 average time/residue: 0.5955 time to fit residues: 106.6184 Evaluate side-chains 156 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 171 optimal weight: 0.0980 chunk 150 optimal weight: 0.0870 chunk 11 optimal weight: 0.8980 chunk 110 optimal weight: 0.0570 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 121 GLN B 165 GLN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN F 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.212117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127889 restraints weight = 25331.944| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.51 r_work: 0.3294 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15613 Z= 0.113 Angle : 0.464 8.513 20940 Z= 0.242 Chirality : 0.037 0.226 2306 Planarity : 0.003 0.054 2566 Dihedral : 16.640 178.985 2735 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.11 % Allowed : 8.78 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.97 (0.20), residues: 1807 helix: 3.71 (0.13), residues: 1269 sheet: -0.93 (0.71), residues: 46 loop : -0.10 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 223 TYR 0.016 0.001 TYR A 47 PHE 0.013 0.001 PHE A 212 TRP 0.019 0.001 TRP D 84 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (15609) covalent geometry : angle 0.46409 / 0.24 (20932) SS BOND : bond 0.00118 / 0.06 ( 4) SS BOND : angle 0.38898 / 0.22 ( 8) hydrogen bonds : bond 0.04481 / 2.94 ( 1126) hydrogen bonds : angle 3.56293 / 2.57 ( 3327) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8213 (mt) cc_final: 0.7859 (mp) REVERT: A 69 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 72 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7470 (tmtm) REVERT: B 44 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8060 (ttp-170) REVERT: B 103 LYS cc_start: 0.7606 (tttm) cc_final: 0.6973 (tttt) REVERT: B 152 MET cc_start: 0.8910 (mtm) cc_final: 0.8667 (mtp) REVERT: C 61 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7932 (mptt) REVERT: D 11 LEU cc_start: 0.7418 (mt) cc_final: 0.7152 (mp) REVERT: D 130 GLU cc_start: 0.8024 (mp0) cc_final: 0.7129 (pm20) REVERT: E 65 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: E 72 LYS cc_start: 0.8265 (tptt) cc_final: 0.7944 (tttp) REVERT: F 1 MET cc_start: 0.5129 (OUTLIER) cc_final: 0.4284 (ttt) REVERT: F 4 ASN cc_start: 0.6259 (p0) cc_final: 0.5871 (t0) REVERT: F 122 LEU cc_start: 0.2361 (OUTLIER) cc_final: 0.2149 (pp) REVERT: G 164 MET cc_start: 0.2306 (ttm) cc_final: 0.2031 (ttp) REVERT: G 214 MET cc_start: 0.1397 (pmm) cc_final: 0.1000 (ttp) REVERT: G 244 MET cc_start: 0.0081 (mtt) cc_final: -0.0510 (tpp) outliers start: 18 outliers final: 4 residues processed: 164 average time/residue: 0.5928 time to fit residues: 106.8379 Evaluate side-chains 152 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 128 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 106 optimal weight: 0.2980 chunk 136 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 121 GLN B 165 GLN C 76 GLN C 121 GLN C 165 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.210121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126204 restraints weight = 27962.033| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.71 r_work: 0.3238 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15613 Z= 0.126 Angle : 0.487 9.163 20940 Z= 0.254 Chirality : 0.037 0.218 2306 Planarity : 0.004 0.054 2566 Dihedral : 16.481 178.808 2735 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.80 % Allowed : 9.59 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.99 (0.20), residues: 1807 helix: 3.72 (0.13), residues: 1264 sheet: -0.89 (0.71), residues: 46 loop : -0.05 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 223 TYR 0.018 0.001 TYR B 208 PHE 0.016 0.001 PHE A 181 TRP 0.015 0.001 TRP A 84 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (15609) covalent geometry : angle 0.48711 / 0.25 (20932) SS BOND : bond 0.00142 / 0.07 ( 4) SS BOND : angle 0.43459 / 0.24 ( 8) hydrogen bonds : bond 0.04805 / 3.13 ( 1126) hydrogen bonds : angle 3.65152 / 2.63 ( 3327) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8263 (mt) cc_final: 0.7920 (mp) REVERT: A 72 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7542 (tmtm) REVERT: B 44 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8109 (ttp-170) REVERT: B 69 GLU cc_start: 0.7514 (pp20) cc_final: 0.7291 (pp20) REVERT: B 103 LYS cc_start: 0.7632 (tttm) cc_final: 0.7013 (tttt) REVERT: B 152 MET cc_start: 0.8997 (mtm) cc_final: 0.8752 (mtp) REVERT: B 173 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8235 (tm) REVERT: C 61 LYS cc_start: 0.8334 (mmtm) cc_final: 0.7996 (mptt) REVERT: D 11 LEU cc_start: 0.7460 (mt) cc_final: 0.7182 (mp) REVERT: D 130 GLU cc_start: 0.8155 (mp0) cc_final: 0.7224 (pm20) REVERT: E 65 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7293 (tp30) REVERT: E 72 LYS cc_start: 0.8336 (tptt) cc_final: 0.8015 (tttp) REVERT: F 1 MET cc_start: 0.5233 (OUTLIER) cc_final: 0.4391 (ttt) REVERT: F 4 ASN cc_start: 0.6264 (p0) cc_final: 0.5874 (t0) REVERT: F 122 LEU cc_start: 0.2345 (mm) cc_final: 0.2119 (pp) REVERT: F 153 LEU cc_start: 0.1805 (pp) cc_final: 0.1191 (mm) REVERT: G 164 MET cc_start: 0.2388 (ttm) cc_final: 0.1951 (ttp) REVERT: G 214 MET cc_start: 0.1312 (pmm) cc_final: 0.0959 (ttp) REVERT: G 244 MET cc_start: 0.0184 (mtt) cc_final: -0.0439 (tpp) outliers start: 13 outliers final: 4 residues processed: 169 average time/residue: 0.6426 time to fit residues: 118.6653 Evaluate side-chains 158 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 145 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 121 GLN B 165 GLN C 121 GLN C 165 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.207828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121798 restraints weight = 21533.604| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.15 r_work: 0.3215 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15613 Z= 0.155 Angle : 0.539 9.584 20940 Z= 0.280 Chirality : 0.040 0.218 2306 Planarity : 0.004 0.053 2566 Dihedral : 16.740 179.951 2735 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.93 % Allowed : 9.77 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.20), residues: 1807 helix: 3.56 (0.13), residues: 1265 sheet: -1.10 (0.71), residues: 46 loop : -0.17 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 223 TYR 0.025 0.002 TYR B 208 PHE 0.020 0.002 PHE A 181 TRP 0.015 0.002 TRP A 84 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (15609) covalent geometry : angle 0.53919 / 0.28 (20932) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 0.49476 / 0.28 ( 8) hydrogen bonds : bond 0.05336 / 3.46 ( 1126) hydrogen bonds : angle 3.82783 / 2.76 ( 3327) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8265 (mt) cc_final: 0.7926 (mp) REVERT: A 72 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7543 (tmtm) REVERT: B 44 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8524 (mtp180) REVERT: B 60 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7592 (tp30) REVERT: B 69 GLU cc_start: 0.7434 (pp20) cc_final: 0.7233 (pp20) REVERT: B 77 ARG cc_start: 0.6340 (tmm-80) cc_final: 0.5797 (ttt180) REVERT: B 152 MET cc_start: 0.9002 (mtm) cc_final: 0.8748 (mtp) REVERT: B 173 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8320 (tm) REVERT: C 61 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8104 (mptt) REVERT: D 11 LEU cc_start: 0.7576 (mt) cc_final: 0.7310 (mp) REVERT: D 130 GLU cc_start: 0.8144 (mp0) cc_final: 0.7169 (pm20) REVERT: E 65 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: E 72 LYS cc_start: 0.8343 (tptt) cc_final: 0.8015 (tttp) REVERT: F 1 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.4436 (ttt) REVERT: F 153 LEU cc_start: 0.1960 (pp) cc_final: 0.1358 (mm) REVERT: G 4 ASN cc_start: 0.6973 (OUTLIER) cc_final: 0.6699 (t0) REVERT: G 51 GLN cc_start: 0.6643 (mt0) cc_final: 0.5929 (mt0) REVERT: G 52 ARG cc_start: 0.6518 (mtm-85) cc_final: 0.6280 (ttm-80) REVERT: G 164 MET cc_start: 0.2432 (ttm) cc_final: 0.2024 (ttp) REVERT: G 214 MET cc_start: 0.1452 (pmm) cc_final: 0.0971 (ttp) REVERT: G 244 MET cc_start: 0.0177 (mtt) cc_final: -0.0457 (tpp) outliers start: 15 outliers final: 5 residues processed: 164 average time/residue: 0.6548 time to fit residues: 117.2195 Evaluate side-chains 162 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 121 GLN B 165 GLN C 76 GLN C 121 GLN C 165 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.208165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122084 restraints weight = 22160.104| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.18 r_work: 0.3213 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15613 Z= 0.152 Angle : 0.537 10.806 20940 Z= 0.277 Chirality : 0.039 0.248 2306 Planarity : 0.004 0.054 2566 Dihedral : 16.751 179.360 2735 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.74 % Allowed : 10.02 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.71 (0.20), residues: 1807 helix: 3.52 (0.13), residues: 1266 sheet: -0.66 (0.78), residues: 38 loop : -0.22 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 223 TYR 0.025 0.002 TYR B 208 PHE 0.019 0.002 PHE A 181 TRP 0.015 0.002 TRP A 84 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15609) covalent geometry : angle 0.53723 / 0.28 (20932) SS BOND : bond 0.00173 / 0.09 ( 4) SS BOND : angle 0.54459 / 0.30 ( 8) hydrogen bonds : bond 0.05255 / 3.41 ( 1126) hydrogen bonds : angle 3.79387 / 2.73 ( 3327) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7527 (tmtm) REVERT: B 44 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8520 (mtp180) REVERT: B 60 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7596 (tp30) REVERT: B 69 GLU cc_start: 0.7405 (pp20) cc_final: 0.7198 (pp20) REVERT: B 77 ARG cc_start: 0.6347 (tmm-80) cc_final: 0.5807 (ttt180) REVERT: B 152 MET cc_start: 0.8995 (mtm) cc_final: 0.8737 (mtp) REVERT: B 173 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8323 (tm) REVERT: C 61 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8084 (mptt) REVERT: D 11 LEU cc_start: 0.7652 (mt) cc_final: 0.7397 (mp) REVERT: D 130 GLU cc_start: 0.8147 (mp0) cc_final: 0.7120 (pm20) REVERT: E 65 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: E 72 LYS cc_start: 0.8327 (tptt) cc_final: 0.8002 (tttp) REVERT: F 1 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.4292 (ttt) REVERT: F 153 LEU cc_start: 0.2017 (pp) cc_final: 0.1426 (mm) REVERT: G 4 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6620 (t0) REVERT: G 51 GLN cc_start: 0.6641 (mt0) cc_final: 0.5916 (mt0) REVERT: G 52 ARG cc_start: 0.6625 (mtm-85) cc_final: 0.6371 (ttm-80) REVERT: G 106 LEU cc_start: -0.0019 (mt) cc_final: -0.0631 (tp) REVERT: G 164 MET cc_start: 0.2420 (ttm) cc_final: 0.2063 (ttp) REVERT: G 214 MET cc_start: 0.1525 (pmm) cc_final: 0.1002 (ttp) REVERT: G 244 MET cc_start: 0.0218 (mtt) cc_final: -0.0412 (tpp) outliers start: 12 outliers final: 5 residues processed: 163 average time/residue: 0.6491 time to fit residues: 115.7200 Evaluate side-chains 164 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 113 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 177 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 121 GLN B 165 GLN C 121 GLN C 165 GLN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.206275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121698 restraints weight = 20060.091| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.49 r_work: 0.3250 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15613 Z= 0.169 Angle : 0.566 10.398 20940 Z= 0.293 Chirality : 0.041 0.249 2306 Planarity : 0.004 0.053 2566 Dihedral : 17.051 179.697 2735 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.87 % Allowed : 9.96 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.19), residues: 1807 helix: 3.37 (0.13), residues: 1272 sheet: -0.72 (0.77), residues: 38 loop : -0.33 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 223 TYR 0.030 0.002 TYR B 208 PHE 0.022 0.002 PHE A 181 TRP 0.016 0.002 TRP B 84 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (15609) covalent geometry : angle 0.56570 / 0.29 (20932) SS BOND : bond 0.00190 / 0.10 ( 4) SS BOND : angle 0.61125 / 0.34 ( 8) hydrogen bonds : bond 0.05548 / 3.60 ( 1126) hydrogen bonds : angle 3.89320 / 2.80 ( 3327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8789.77 seconds wall clock time: 149 minutes 41.83 seconds (8981.83 seconds total)