Starting phenix.real_space_refine on Sun Aug 24 01:45:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyk_18756/08_2025/8qyk_18756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyk_18756/08_2025/8qyk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyk_18756/08_2025/8qyk_18756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyk_18756/08_2025/8qyk_18756.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyk_18756/08_2025/8qyk_18756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyk_18756/08_2025/8qyk_18756.cif" } 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-2.0-5787/lib/python3.9/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, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 4.39, per 1000 atoms: 0.27 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: 1.13 Conformation dependent library (CDL) restraints added in 648.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.33 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: 2.32 Time building geometry restraints manager: 1.46 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: 9192 32.97 - 65.94: 377 65.94 - 98.90: 37 98.90 - 131.87: 19 131.87 - 164.84: 12 Dihedral angle restraints: 9637 sinusoidal: 4286 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 9634 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: 9.980 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.240 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.008 0.170 15613 Z= 0.419 Angle : 1.373 52.057 20940 Z= 0.530 Chirality : 0.048 0.553 2306 Planarity : 0.012 0.461 2566 Dihedral : 18.956 164.839 6149 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 aren 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 covalent geometry : bond 0.00825 (15609) covalent geometry : angle 1.37271 (20932) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.79722 ( 8) hydrogen bonds : bond 0.10687 ( 1126) hydrogen bonds : angle 4.52773 ( 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 : 0.732 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: 0.7805 time to fit residues: 152.9893 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 : 0.639 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4348 r_free = 0.4348 target = 0.209066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123558 restraints weight = 19908.661| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.53 r_work: 0.3275 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15613 Z= 0.148 Angle : 0.531 8.003 20940 Z= 0.276 Chirality : 0.039 0.162 2306 Planarity : 0.004 0.049 2566 Dihedral : 18.938 177.477 2659 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.68 % Allowed : 4.82 % Favored : 94.50 % 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 aren not related in a simple way. whole: 3.64 (0.20), residues: 1807 helix: 3.47 (0.13), residues: 1267 sheet: -0.96 (0.76), residues: 46 loop : -0.23 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 77 TYR 0.021 0.002 TYR B 208 PHE 0.018 0.002 PHE A 181 TRP 0.017 0.002 TRP D 84 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00312 (15609) covalent geometry : angle 0.53040 (20932) SS BOND : bond 0.00109 ( 4) SS BOND : angle 0.77635 ( 8) hydrogen bonds : bond 0.05430 ( 1126) hydrogen bonds : angle 3.96752 ( 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 169 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3463 (mtp) cc_final: 0.3213 (ttt) REVERT: B 44 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8028 (ttp-170) REVERT: B 102 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6946 (mm-30) REVERT: B 152 MET cc_start: 0.9084 (mtm) cc_final: 0.8866 (mtp) REVERT: C 11 LEU cc_start: 0.8614 (mt) cc_final: 0.8379 (mt) REVERT: C 61 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8160 (mptt) REVERT: D 130 GLU cc_start: 0.8132 (mp0) cc_final: 0.7289 (pm20) REVERT: E 65 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: F 4 ASN cc_start: 0.6330 (p0) cc_final: 0.6046 (t0) REVERT: F 122 LEU cc_start: 0.2377 (mm) cc_final: 0.2144 (pp) REVERT: F 244 MET cc_start: 0.1449 (ptp) cc_final: 0.1226 (pmm) REVERT: G 11 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5654 (ptp90) REVERT: G 51 GLN cc_start: 0.6990 (mt0) cc_final: 0.6594 (mt0) REVERT: G 164 MET cc_start: 0.2747 (ttm) cc_final: 0.2187 (ttp) REVERT: G 244 MET cc_start: 0.0365 (mtt) cc_final: 0.0147 (tpp) outliers start: 11 outliers final: 5 residues processed: 164 average time/residue: 0.6761 time to fit residues: 120.6722 Evaluate side-chains 151 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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: 6.9990 chunk 137 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 117 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 165 GLN C 121 GLN E 171 ASN F 87 HIS ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.206121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121151 restraints weight = 17780.186| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.45 r_work: 0.3254 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 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 = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15613 Z= 0.176 Angle : 0.568 8.874 20940 Z= 0.296 Chirality : 0.041 0.177 2306 Planarity : 0.004 0.057 2566 Dihedral : 18.341 178.500 2659 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.93 % Allowed : 6.80 % Favored : 92.27 % 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 aren not related in a simple way. whole: 3.50 (0.19), residues: 1807 helix: 3.32 (0.13), residues: 1266 sheet: -1.14 (0.74), residues: 46 loop : -0.13 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 223 TYR 0.027 0.002 TYR B 208 PHE 0.024 0.002 PHE A 181 TRP 0.021 0.002 TRP B 84 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00385 (15609) covalent geometry : angle 0.56830 (20932) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.73721 ( 8) hydrogen bonds : bond 0.05809 ( 1126) hydrogen bonds : angle 4.04105 ( 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 177 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8597 (mtpt) REVERT: B 69 GLU cc_start: 0.7555 (pp20) cc_final: 0.7336 (pp20) REVERT: B 102 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 152 MET cc_start: 0.9062 (mtm) cc_final: 0.8788 (mtp) REVERT: B 167 SER cc_start: 0.8653 (m) cc_final: 0.8348 (t) REVERT: C 61 LYS cc_start: 0.8453 (mmtm) cc_final: 0.8202 (mptt) REVERT: D 257 MET cc_start: 0.3179 (OUTLIER) cc_final: 0.1855 (mtp) REVERT: E 65 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: E 72 LYS cc_start: 0.8379 (tptt) cc_final: 0.8089 (tttp) REVERT: F 1 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4591 (ttt) REVERT: F 4 ASN cc_start: 0.6419 (p0) cc_final: 0.6160 (t0) REVERT: G 164 MET cc_start: 0.2379 (ttm) cc_final: 0.1865 (ttp) REVERT: G 244 MET cc_start: 0.0475 (mtt) cc_final: 0.0255 (tpp) outliers start: 15 outliers final: 4 residues processed: 168 average time/residue: 0.6984 time to fit residues: 127.4062 Evaluate side-chains 154 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 D residue 257 MET Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET 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: 0.6980 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4336 r_free = 0.4336 target = 0.208129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124311 restraints weight = 29431.567| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.74 r_work: 0.3223 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 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 = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 0.059 15613 Z= 0.135 Angle : 0.502 7.690 20940 Z= 0.262 Chirality : 0.038 0.224 2306 Planarity : 0.004 0.058 2566 Dihedral : 17.585 178.669 2655 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.87 % Allowed : 8.23 % Favored : 90.91 % 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 aren not related in a simple way. whole: 3.73 (0.20), residues: 1807 helix: 3.49 (0.13), residues: 1264 sheet: -1.12 (0.75), residues: 46 loop : -0.01 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.018 0.001 TYR B 208 PHE 0.016 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 covalent geometry : bond 0.00282 (15609) covalent geometry : angle 0.50239 (20932) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.58379 ( 8) hydrogen bonds : bond 0.05131 ( 1126) hydrogen bonds : angle 3.84335 ( 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 170 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8142 (ttp-170) REVERT: B 61 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8623 (mtpt) REVERT: B 69 GLU cc_start: 0.7569 (pp20) cc_final: 0.7314 (pp20) REVERT: B 102 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7156 (mm-30) REVERT: B 152 MET cc_start: 0.9058 (mtm) cc_final: 0.8803 (mtp) REVERT: C 61 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8088 (mptt) REVERT: D 130 GLU cc_start: 0.8215 (mp0) cc_final: 0.7349 (pm20) REVERT: E 65 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: E 72 LYS cc_start: 0.8385 (tptt) cc_final: 0.8069 (tttp) REVERT: F 1 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.4683 (ttt) REVERT: F 4 ASN cc_start: 0.6169 (p0) cc_final: 0.5802 (t0) REVERT: F 122 LEU cc_start: 0.2404 (mm) cc_final: 0.2146 (pp) REVERT: F 140 GLU cc_start: 0.3497 (mp0) cc_final: 0.3227 (tm-30) REVERT: G 164 MET cc_start: 0.2192 (ttm) cc_final: 0.1741 (ttp) outliers start: 14 outliers final: 4 residues processed: 161 average time/residue: 0.6364 time to fit residues: 111.9646 Evaluate side-chains 157 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 122 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 147 optimal weight: 0.0970 chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN D 121 GLN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN G 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.208182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123058 restraints weight = 22628.640| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.35 r_work: 0.3248 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 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 = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15613 Z= 0.132 Angle : 0.495 8.195 20940 Z= 0.259 Chirality : 0.038 0.229 2306 Planarity : 0.004 0.058 2566 Dihedral : 17.142 177.770 2655 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.80 % Allowed : 8.78 % 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 aren not related in a simple way. whole: 3.81 (0.19), residues: 1807 helix: 3.56 (0.13), residues: 1264 sheet: -1.04 (0.74), residues: 46 loop : -0.01 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 223 TYR 0.021 0.001 TYR B 208 PHE 0.017 0.001 PHE A 181 TRP 0.017 0.001 TRP A 84 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00275 (15609) covalent geometry : angle 0.49522 (20932) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.59163 ( 8) hydrogen bonds : bond 0.05066 ( 1126) hydrogen bonds : angle 3.78758 ( 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 171 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8308 (mt) cc_final: 0.7970 (mp) REVERT: B 61 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8619 (mtpt) REVERT: B 69 GLU cc_start: 0.7529 (pp20) cc_final: 0.7270 (pp20) REVERT: B 102 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 152 MET cc_start: 0.9028 (mtm) cc_final: 0.8789 (mtp) REVERT: C 61 LYS cc_start: 0.8395 (mmtm) cc_final: 0.8069 (mptt) REVERT: D 11 LEU cc_start: 0.7625 (mt) cc_final: 0.7327 (mp) REVERT: D 130 GLU cc_start: 0.8125 (mp0) cc_final: 0.7270 (pm20) REVERT: E 65 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: E 72 LYS cc_start: 0.8352 (tptt) cc_final: 0.8038 (tttp) REVERT: F 1 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.4633 (ttt) REVERT: F 4 ASN cc_start: 0.6328 (p0) cc_final: 0.6005 (t0) REVERT: G 164 MET cc_start: 0.2486 (ttm) cc_final: 0.2105 (ttp) REVERT: G 214 MET cc_start: 0.1497 (pmm) cc_final: 0.1019 (ttp) REVERT: G 244 MET cc_start: 0.0635 (tpp) cc_final: 0.0285 (tpp) outliers start: 13 outliers final: 2 residues processed: 162 average time/residue: 0.6511 time to fit residues: 114.9717 Evaluate side-chains 155 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 145 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN G 51 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.208592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122902 restraints weight = 26893.045| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.58 r_work: 0.3212 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1767 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= 0.133 Angle : 0.499 8.543 20940 Z= 0.261 Chirality : 0.038 0.227 2306 Planarity : 0.004 0.056 2566 Dihedral : 16.905 177.557 2655 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.11 % Allowed : 8.91 % Favored : 89.98 % 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 aren not related in a simple way. whole: 3.81 (0.19), residues: 1807 helix: 3.56 (0.13), residues: 1264 sheet: -1.00 (0.73), residues: 46 loop : -0.01 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 223 TYR 0.021 0.001 TYR B 208 PHE 0.017 0.001 PHE A 181 TRP 0.017 0.002 TRP B 84 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00281 (15609) covalent geometry : angle 0.49866 (20932) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.60311 ( 8) hydrogen bonds : bond 0.05074 ( 1126) hydrogen bonds : angle 3.78289 ( 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 172 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8066 (ttp-170) REVERT: B 61 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8623 (mtpt) REVERT: B 69 GLU cc_start: 0.7553 (pp20) cc_final: 0.7273 (pp20) REVERT: B 77 ARG cc_start: 0.6238 (tmm-80) cc_final: 0.5663 (ttt180) REVERT: B 102 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7171 (mm-30) REVERT: B 152 MET cc_start: 0.9017 (mtm) cc_final: 0.8769 (mtp) REVERT: C 61 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8034 (mptt) REVERT: D 11 LEU cc_start: 0.7594 (mt) cc_final: 0.7304 (mp) REVERT: D 130 GLU cc_start: 0.8167 (mp0) cc_final: 0.7180 (pm20) REVERT: E 65 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: E 72 LYS cc_start: 0.8343 (tptt) cc_final: 0.8009 (tttp) REVERT: F 1 MET cc_start: 0.5256 (OUTLIER) cc_final: 0.4283 (ttt) REVERT: F 4 ASN cc_start: 0.6284 (p0) cc_final: 0.5894 (t0) REVERT: F 122 LEU cc_start: 0.2288 (mm) cc_final: 0.2063 (pp) REVERT: G 164 MET cc_start: 0.2431 (ttm) cc_final: 0.2068 (ttp) REVERT: G 244 MET cc_start: 0.0501 (tpp) cc_final: 0.0182 (tpp) outliers start: 18 outliers final: 5 residues processed: 163 average time/residue: 0.6405 time to fit residues: 114.3542 Evaluate side-chains 161 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER 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 C residue 175 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET 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: 0.0980 chunk 171 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 110 optimal weight: 0.0870 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN F 158 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.209753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123801 restraints weight = 24921.040| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.46 r_work: 0.3239 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 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 = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 15613 Z= 0.121 Angle : 0.482 9.317 20940 Z= 0.251 Chirality : 0.038 0.279 2306 Planarity : 0.004 0.055 2566 Dihedral : 16.542 179.623 2655 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.05 % Allowed : 9.28 % Favored : 89.67 % 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 aren not related in a simple way. whole: 3.92 (0.20), residues: 1807 helix: 3.66 (0.13), residues: 1264 sheet: -0.90 (0.72), residues: 46 loop : -0.04 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 223 TYR 0.020 0.001 TYR A 17 PHE 0.015 0.001 PHE A 181 TRP 0.017 0.001 TRP D 84 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00249 (15609) covalent geometry : angle 0.48226 (20932) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.56679 ( 8) hydrogen bonds : bond 0.04779 ( 1126) hydrogen bonds : angle 3.68993 ( 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 173 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8281 (mt) cc_final: 0.7946 (mp) REVERT: B 61 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8593 (mtpt) REVERT: B 69 GLU cc_start: 0.7559 (pp20) cc_final: 0.7284 (pp20) REVERT: B 102 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7211 (mm-30) REVERT: B 152 MET cc_start: 0.8957 (mtm) cc_final: 0.8707 (mtp) REVERT: C 61 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8025 (mptt) REVERT: D 11 LEU cc_start: 0.7509 (mt) cc_final: 0.7244 (mp) REVERT: D 130 GLU cc_start: 0.8094 (mp0) cc_final: 0.7189 (pm20) REVERT: E 65 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: E 72 LYS cc_start: 0.8314 (tptt) cc_final: 0.7978 (tttp) REVERT: F 1 MET cc_start: 0.5196 (OUTLIER) cc_final: 0.4363 (ttt) REVERT: F 4 ASN cc_start: 0.6277 (p0) cc_final: 0.5881 (t0) REVERT: F 122 LEU cc_start: 0.2255 (mm) cc_final: 0.2035 (pp) REVERT: G 164 MET cc_start: 0.2466 (ttm) cc_final: 0.2105 (ttp) REVERT: G 214 MET cc_start: 0.1337 (pmm) cc_final: 0.0961 (ttp) REVERT: G 244 MET cc_start: 0.0585 (tpp) cc_final: 0.0279 (tpp) outliers start: 17 outliers final: 3 residues processed: 163 average time/residue: 0.6248 time to fit residues: 111.6189 Evaluate side-chains 157 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 128 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 130 optimal weight: 0.0970 chunk 171 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN G 51 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.209188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123385 restraints weight = 27673.580| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.59 r_work: 0.3220 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 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 = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15613 Z= 0.127 Angle : 0.490 8.999 20940 Z= 0.256 Chirality : 0.038 0.242 2306 Planarity : 0.004 0.054 2566 Dihedral : 16.423 179.796 2655 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.05 % Allowed : 9.52 % Favored : 89.42 % 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 aren not related in a simple way. whole: 3.90 (0.20), residues: 1807 helix: 3.66 (0.13), residues: 1261 sheet: -0.91 (0.71), residues: 46 loop : -0.08 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 223 TYR 0.019 0.002 TYR B 208 PHE 0.016 0.001 PHE A 181 TRP 0.016 0.001 TRP D 84 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00266 (15609) covalent geometry : angle 0.49025 (20932) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.57778 ( 8) hydrogen bonds : bond 0.04910 ( 1126) hydrogen bonds : angle 3.70915 ( 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: 17 poor density : 156 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8257 (mt) cc_final: 0.7918 (mp) REVERT: B 44 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8084 (ttp-170) REVERT: B 61 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8628 (mtpt) REVERT: B 69 GLU cc_start: 0.7612 (pp20) cc_final: 0.7330 (pp20) REVERT: B 102 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 152 MET cc_start: 0.8996 (mtm) cc_final: 0.8745 (mtp) REVERT: C 61 LYS cc_start: 0.8395 (mmtm) cc_final: 0.8047 (mptt) REVERT: D 11 LEU cc_start: 0.7479 (mt) cc_final: 0.7206 (mp) REVERT: D 130 GLU cc_start: 0.8140 (mp0) cc_final: 0.7226 (pm20) REVERT: E 65 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: E 72 LYS cc_start: 0.8328 (tptt) cc_final: 0.7995 (tttp) REVERT: F 1 MET cc_start: 0.5320 (OUTLIER) cc_final: 0.4459 (ttt) REVERT: F 4 ASN cc_start: 0.6284 (p0) cc_final: 0.5884 (t0) REVERT: F 122 LEU cc_start: 0.2239 (mm) cc_final: 0.2027 (pp) REVERT: F 153 LEU cc_start: 0.2243 (tp) cc_final: 0.1837 (mm) REVERT: G 164 MET cc_start: 0.2344 (ttm) cc_final: 0.1972 (ttp) REVERT: G 214 MET cc_start: 0.1169 (pmm) cc_final: 0.0839 (ttp) REVERT: G 244 MET cc_start: 0.0554 (tpp) cc_final: 0.0199 (tpp) outliers start: 17 outliers final: 6 residues processed: 165 average time/residue: 0.6692 time to fit residues: 120.4154 Evaluate side-chains 160 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER 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 C residue 14 VAL Chi-restraints excluded: chain C residue 175 ARG 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 G residue 4 ASN 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: 0.7980 chunk 29 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.207908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122172 restraints weight = 21447.142| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.60 r_work: 0.3230 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 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 = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1941 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= 0.146 Angle : 0.521 9.634 20940 Z= 0.272 Chirality : 0.039 0.245 2306 Planarity : 0.004 0.054 2566 Dihedral : 16.574 179.862 2655 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.93 % Allowed : 9.71 % Favored : 89.36 % 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 aren not related in a simple way. whole: 3.72 (0.20), residues: 1807 helix: 3.52 (0.13), residues: 1266 sheet: -0.98 (0.70), residues: 46 loop : -0.16 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 223 TYR 0.024 0.002 TYR B 208 PHE 0.019 0.002 PHE A 181 TRP 0.016 0.002 TRP B 84 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00314 (15609) covalent geometry : angle 0.52104 (20932) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.60559 ( 8) hydrogen bonds : bond 0.05232 ( 1126) hydrogen bonds : angle 3.80219 ( 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 171 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8514 (mtp180) REVERT: B 61 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8630 (mtpt) REVERT: B 69 GLU cc_start: 0.7566 (pp20) cc_final: 0.7293 (pp20) REVERT: B 102 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7292 (mm-30) REVERT: B 152 MET cc_start: 0.8990 (mtm) cc_final: 0.8735 (mtp) REVERT: B 173 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8390 (tm) REVERT: C 61 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8122 (mptt) REVERT: D 11 LEU cc_start: 0.7637 (mt) cc_final: 0.7367 (mp) REVERT: D 130 GLU cc_start: 0.8129 (mp0) cc_final: 0.7181 (pm20) REVERT: E 65 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: E 72 LYS cc_start: 0.8342 (tptt) cc_final: 0.8027 (tttp) REVERT: F 1 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.4254 (ttt) REVERT: F 4 ASN cc_start: 0.6332 (p0) cc_final: 0.6036 (t0) REVERT: G 51 GLN cc_start: 0.6619 (mt0) cc_final: 0.5908 (mt0) REVERT: G 52 ARG cc_start: 0.6547 (mtm-85) cc_final: 0.6305 (ttm-80) REVERT: G 106 LEU cc_start: -0.0071 (mt) cc_final: -0.0678 (tp) REVERT: G 214 MET cc_start: 0.1510 (pmm) cc_final: 0.1060 (ttp) REVERT: G 244 MET cc_start: 0.0438 (tpp) cc_final: 0.0119 (tpp) outliers start: 15 outliers final: 8 residues processed: 164 average time/residue: 0.6514 time to fit residues: 116.2684 Evaluate side-chains 167 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER 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 B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 175 ARG 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: 0.6980 chunk 82 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 161 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 112 optimal weight: 0.3980 chunk 151 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN C 165 GLN 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 = 0.4343 r_free = 0.4343 target = 0.209288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123972 restraints weight = 22095.768| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.62 r_work: 0.3260 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2020 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= 0.124 Angle : 0.499 9.601 20940 Z= 0.259 Chirality : 0.038 0.247 2306 Planarity : 0.004 0.054 2566 Dihedral : 16.354 178.888 2655 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.80 % Allowed : 10.27 % Favored : 88.93 % 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 aren not related in a simple way. whole: 3.87 (0.20), residues: 1807 helix: 3.63 (0.13), residues: 1263 sheet: -1.05 (0.72), residues: 46 loop : -0.06 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 223 TYR 0.021 0.001 TYR A 17 PHE 0.015 0.001 PHE A 181 TRP 0.018 0.001 TRP D 84 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00259 (15609) covalent geometry : angle 0.49889 (20932) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.52259 ( 8) hydrogen bonds : bond 0.04844 ( 1126) hydrogen bonds : angle 3.69982 ( 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 169 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8030 (ttp-170) REVERT: B 61 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8590 (mtpt) REVERT: B 69 GLU cc_start: 0.7588 (pp20) cc_final: 0.7328 (pp20) REVERT: B 102 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7279 (mm-30) REVERT: B 152 MET cc_start: 0.8949 (mtm) cc_final: 0.8691 (mtp) REVERT: B 173 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8319 (tm) REVERT: C 61 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8096 (mptt) REVERT: D 11 LEU cc_start: 0.7543 (mt) cc_final: 0.7288 (mp) REVERT: D 130 GLU cc_start: 0.8074 (mp0) cc_final: 0.7202 (pm20) REVERT: E 65 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: E 72 LYS cc_start: 0.8312 (tptt) cc_final: 0.7999 (tttp) REVERT: F 1 MET cc_start: 0.5283 (OUTLIER) cc_final: 0.4411 (ttt) REVERT: F 4 ASN cc_start: 0.6315 (p0) cc_final: 0.6009 (t0) REVERT: F 153 LEU cc_start: 0.2317 (tp) cc_final: 0.1889 (mm) REVERT: G 51 GLN cc_start: 0.6631 (mt0) cc_final: 0.5943 (mt0) REVERT: G 52 ARG cc_start: 0.6509 (mtm-85) cc_final: 0.6290 (ttm-80) REVERT: G 106 LEU cc_start: -0.0111 (mt) cc_final: -0.0685 (tp) REVERT: G 214 MET cc_start: 0.1486 (pmm) cc_final: 0.1021 (ttp) REVERT: G 244 MET cc_start: 0.0470 (tpp) cc_final: 0.0162 (tpp) outliers start: 13 outliers final: 6 residues processed: 164 average time/residue: 0.6874 time to fit residues: 122.9692 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 : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER 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 C residue 175 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 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: 0.9980 chunk 81 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN C 121 GLN C 165 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS 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 = 0.4304 r_free = 0.4304 target = 0.205411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119698 restraints weight = 19876.971| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.54 r_work: 0.3198 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15613 Z= 0.234 Angle : 0.635 10.153 20940 Z= 0.331 Chirality : 0.045 0.242 2306 Planarity : 0.005 0.052 2566 Dihedral : 17.346 177.975 2655 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.93 % Allowed : 10.08 % Favored : 88.99 % 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 aren not related in a simple way. whole: 3.23 (0.19), residues: 1807 helix: 3.13 (0.13), residues: 1270 sheet: -1.09 (0.62), residues: 57 loop : -0.27 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 223 TYR 0.039 0.003 TYR B 208 PHE 0.029 0.003 PHE A 181 TRP 0.018 0.003 TRP B 84 HIS 0.009 0.002 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00532 (15609) covalent geometry : angle 0.63499 (20932) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.81410 ( 8) hydrogen bonds : bond 0.06154 ( 1126) hydrogen bonds : angle 4.06725 ( 3327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9670.78 seconds wall clock time: 164 minutes 34.94 seconds (9874.94 seconds total)