Starting phenix.real_space_refine on Sat Jun 14 11:55:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyk_18756/06_2025/8qyk_18756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyk_18756/06_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_18756/06_2025/8qyk_18756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyk_18756/06_2025/8qyk_18756.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyk_18756/06_2025/8qyk_18756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyk_18756/06_2025/8qyk_18756.cif" } resolution = 2.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.095 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.49, per 1000 atoms: 0.90 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: 4.49 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.46 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: 4.92 Time building geometry restraints manager: 5.19 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 265 or resid 501 through 503)) selection = (chain 'B' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 265 or resid 501 through 503)) selection = (chain 'C' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 265 or resid 501 through 503)) selection = (chain 'D' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 265 or resid 501 through 503)) selection = (chain 'E' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 265 or resid 501 through 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: 0.010 Normalize map: mean=0, sd=1: 11.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 43.310 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (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 TRP 0.018 0.002 TRP A 84 HIS 0.005 0.001 HIS D 82 PHE 0.021 0.002 PHE A 181 TYR 0.023 0.002 TYR E 208 ARG 0.008 0.001 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.10687 ( 1126) hydrogen bonds : angle 4.52773 ( 3327) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.79722 ( 8) covalent geometry : bond 0.00825 (15609) covalent geometry : angle 1.37271 (20932) *********************** 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 : 1.753 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: 0.1452 (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: 0.2373 (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: 1.8177 time to fit residues: 356.4413 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 : 1.961 ------------------------------------------------------------------------------- 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 150 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 161 optimal weight: 0.2980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 E 171 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.207539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120685 restraints weight = 21016.353| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.03 r_work: 0.3232 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15613 Z= 0.173 Angle : 0.564 8.136 20940 Z= 0.293 Chirality : 0.041 0.168 2306 Planarity : 0.004 0.056 2566 Dihedral : 19.172 177.099 2659 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.74 % Allowed : 4.82 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.20), residues: 1807 helix: 3.34 (0.13), residues: 1272 sheet: -1.40 (0.82), residues: 36 loop : -0.30 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 84 HIS 0.006 0.001 HIS B 82 PHE 0.022 0.002 PHE A 181 TYR 0.024 0.002 TYR B 208 ARG 0.005 0.001 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.05749 ( 1126) hydrogen bonds : angle 4.06078 ( 3327) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.83510 ( 8) covalent geometry : bond 0.00377 (15609) covalent geometry : angle 0.56421 (20932) *********************** 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 170 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3416 (mtp) cc_final: 0.3148 (ttt) REVERT: B 44 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8025 (ttp-170) REVERT: B 61 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8544 (mtpt) REVERT: B 102 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6859 (mm-30) REVERT: B 152 MET cc_start: 0.9104 (mtm) cc_final: 0.8835 (mtp) REVERT: C 11 LEU cc_start: 0.8605 (mt) cc_final: 0.8362 (mt) REVERT: C 61 LYS cc_start: 0.8482 (mmtm) cc_final: 0.8153 (mptt) REVERT: D 130 GLU cc_start: 0.8196 (mp0) cc_final: 0.7308 (pm20) REVERT: E 65 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: F 122 LEU cc_start: 0.2352 (mm) cc_final: 0.2128 (pp) REVERT: F 244 MET cc_start: 0.1449 (ptp) cc_final: 0.1239 (pmm) REVERT: G 11 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5459 (ptp-170) REVERT: G 164 MET cc_start: 0.2837 (ttm) cc_final: 0.2335 (ttp) REVERT: G 244 MET cc_start: 0.0425 (mtt) cc_final: 0.0184 (tpp) outliers start: 12 outliers final: 5 residues processed: 164 average time/residue: 2.1280 time to fit residues: 382.4177 Evaluate side-chains 153 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 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 121 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN C 121 GLN C 165 GLN E 171 ASN F 87 HIS 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 = 0.4341 r_free = 0.4341 target = 0.208699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122896 restraints weight = 23343.287| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.29 r_work: 0.3255 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 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 = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1321 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= 0.134 Angle : 0.498 8.885 20940 Z= 0.260 Chirality : 0.038 0.159 2306 Planarity : 0.004 0.055 2566 Dihedral : 17.969 179.591 2659 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.87 % Allowed : 6.56 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.20), residues: 1807 helix: 3.52 (0.13), residues: 1264 sheet: -1.09 (0.74), residues: 46 loop : -0.04 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 84 HIS 0.005 0.001 HIS D 82 PHE 0.016 0.001 PHE A 181 TYR 0.021 0.001 TYR B 208 ARG 0.003 0.000 ARG G 223 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 1126) hydrogen bonds : angle 3.83325 ( 3327) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.68019 ( 8) covalent geometry : bond 0.00277 (15609) covalent geometry : angle 0.49762 (20932) *********************** 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 182 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3218 (mtp) cc_final: 0.3005 (ttt) REVERT: B 69 GLU cc_start: 0.7473 (pp20) cc_final: 0.7248 (pp20) REVERT: B 102 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7016 (mm-30) REVERT: B 152 MET cc_start: 0.9047 (mtm) cc_final: 0.8792 (mtp) REVERT: B 165 GLN cc_start: 0.8130 (mt0) cc_final: 0.7930 (mt0) REVERT: C 11 LEU cc_start: 0.8588 (mt) cc_final: 0.8355 (mt) REVERT: C 61 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8064 (mptt) REVERT: D 130 GLU cc_start: 0.8145 (mp0) cc_final: 0.7277 (pm20) REVERT: D 257 MET cc_start: 0.3044 (OUTLIER) cc_final: 0.1838 (mtp) REVERT: E 65 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: E 72 LYS cc_start: 0.8382 (tptt) cc_final: 0.8080 (tttp) REVERT: F 1 MET cc_start: 0.5360 (OUTLIER) cc_final: 0.4749 (ttt) REVERT: F 4 ASN cc_start: 0.6236 (p0) cc_final: 0.5880 (t0) REVERT: G 11 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5805 (ptp90) REVERT: G 15 GLU cc_start: 0.6051 (tp30) cc_final: 0.5817 (tp30) REVERT: G 51 GLN cc_start: 0.6949 (mt0) cc_final: 0.5069 (mm-40) REVERT: G 164 MET cc_start: 0.2465 (ttm) cc_final: 0.1986 (ttp) REVERT: G 244 MET cc_start: 0.0416 (mtt) cc_final: 0.0201 (tpp) outliers start: 14 outliers final: 3 residues processed: 174 average time/residue: 2.3417 time to fit residues: 446.1179 Evaluate side-chains 157 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 11 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 130 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 166 optimal weight: 0.3980 chunk 111 optimal weight: 0.8980 chunk 152 optimal weight: 0.0020 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 147 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 overall best weight: 0.3966 ------------------------------------------------------------------------------- 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 C 121 GLN E 171 ASN F 158 GLN ** 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 = 0.4362 r_free = 0.4362 target = 0.210515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125879 restraints weight = 24489.764| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.37 r_work: 0.3268 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 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 = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 15613 Z= 0.116 Angle : 0.465 8.284 20940 Z= 0.243 Chirality : 0.037 0.223 2306 Planarity : 0.003 0.057 2566 Dihedral : 17.213 179.049 2659 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.99 % Allowed : 7.42 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.20), residues: 1807 helix: 3.67 (0.13), residues: 1264 sheet: -0.97 (0.73), residues: 46 loop : -0.03 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 84 HIS 0.004 0.001 HIS D 82 PHE 0.014 0.001 PHE A 181 TYR 0.017 0.001 TYR B 208 ARG 0.002 0.000 ARG G 223 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 1126) hydrogen bonds : angle 3.68826 ( 3327) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.49564 ( 8) covalent geometry : bond 0.00233 (15609) covalent geometry : angle 0.46463 (20932) *********************** 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 177 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8285 (mt) cc_final: 0.7946 (mp) REVERT: A 257 MET cc_start: 0.3482 (mtp) cc_final: 0.3099 (ttt) REVERT: B 44 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8143 (ttp-170) REVERT: B 69 GLU cc_start: 0.7602 (pp20) cc_final: 0.7352 (pp20) REVERT: B 102 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 152 MET cc_start: 0.9003 (mtm) cc_final: 0.8782 (mtp) REVERT: B 165 GLN cc_start: 0.8147 (mt0) cc_final: 0.7914 (mt0) REVERT: C 61 LYS cc_start: 0.8341 (mmtm) cc_final: 0.8015 (mptt) REVERT: D 1 MET cc_start: 0.4260 (mtm) cc_final: 0.4040 (mtm) REVERT: D 130 GLU cc_start: 0.8138 (mp0) cc_final: 0.7248 (pm20) REVERT: E 65 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: E 72 LYS cc_start: 0.8400 (tptt) cc_final: 0.8092 (tttp) REVERT: F 1 MET cc_start: 0.5251 (OUTLIER) cc_final: 0.4630 (ttt) REVERT: F 4 ASN cc_start: 0.6221 (p0) cc_final: 0.5827 (t0) REVERT: G 51 GLN cc_start: 0.6855 (mt0) cc_final: 0.6464 (mt0) REVERT: G 164 MET cc_start: 0.2283 (ttm) cc_final: 0.1841 (ttp) REVERT: G 244 MET cc_start: 0.0491 (mtt) cc_final: 0.0189 (tpp) outliers start: 16 outliers final: 3 residues processed: 169 average time/residue: 1.5629 time to fit residues: 288.7256 Evaluate side-chains 159 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG 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 51 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 83 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.0670 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 147 optimal weight: 0.1980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 C 121 GLN E 171 ASN G 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.209278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124496 restraints weight = 23759.896| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.41 r_work: 0.3270 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 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 = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 15613 Z= 0.121 Angle : 0.472 8.281 20940 Z= 0.247 Chirality : 0.037 0.230 2306 Planarity : 0.004 0.056 2566 Dihedral : 16.806 178.632 2655 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.80 % Allowed : 8.47 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.20), residues: 1807 helix: 3.72 (0.13), residues: 1261 sheet: -0.88 (0.73), residues: 46 loop : -0.07 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 84 HIS 0.004 0.001 HIS D 82 PHE 0.015 0.001 PHE A 181 TYR 0.018 0.001 TYR B 208 ARG 0.003 0.000 ARG G 223 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 1126) hydrogen bonds : angle 3.70028 ( 3327) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.51630 ( 8) covalent geometry : bond 0.00246 (15609) covalent geometry : angle 0.47198 (20932) *********************** 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 163 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8245 (mt) cc_final: 0.7900 (mp) REVERT: B 61 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8599 (mtpt) REVERT: B 69 GLU cc_start: 0.7582 (pp20) cc_final: 0.7334 (pp20) REVERT: B 102 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 152 MET cc_start: 0.8989 (mtm) cc_final: 0.8754 (mtp) REVERT: B 165 GLN cc_start: 0.8112 (mt0) cc_final: 0.7885 (mt0) REVERT: C 61 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8063 (mptt) REVERT: D 130 GLU cc_start: 0.8124 (mp0) cc_final: 0.7222 (pm20) REVERT: D 257 MET cc_start: 0.3112 (OUTLIER) cc_final: 0.1865 (mtm) REVERT: E 65 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: E 72 LYS cc_start: 0.8387 (tptt) cc_final: 0.8074 (tttp) REVERT: F 1 MET cc_start: 0.5225 (OUTLIER) cc_final: 0.4537 (ttt) REVERT: F 4 ASN cc_start: 0.6226 (p0) cc_final: 0.5917 (t0) REVERT: G 164 MET cc_start: 0.2445 (ttm) cc_final: 0.2059 (ttp) REVERT: G 214 MET cc_start: 0.1500 (pmm) cc_final: 0.1069 (ttp) REVERT: G 244 MET cc_start: 0.0430 (mtt) cc_final: 0.0133 (tpp) outliers start: 13 outliers final: 3 residues processed: 156 average time/residue: 1.5563 time to fit residues: 265.6869 Evaluate side-chains 153 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 51 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 35 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 83 optimal weight: 0.0370 chunk 136 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 C 121 GLN E 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.209913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125900 restraints weight = 21139.716| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.55 r_work: 0.3296 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1773 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= 0.115 Angle : 0.461 8.343 20940 Z= 0.241 Chirality : 0.037 0.228 2306 Planarity : 0.003 0.054 2566 Dihedral : 16.462 178.886 2655 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.87 % Allowed : 8.84 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.01 (0.20), residues: 1807 helix: 3.76 (0.13), residues: 1261 sheet: -0.72 (0.73), residues: 46 loop : -0.10 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 84 HIS 0.004 0.001 HIS D 82 PHE 0.014 0.001 PHE A 181 TYR 0.016 0.001 TYR B 208 ARG 0.003 0.000 ARG G 223 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 1126) hydrogen bonds : angle 3.64196 ( 3327) SS BOND : bond 0.00133 ( 4) SS BOND : angle 0.51289 ( 8) covalent geometry : bond 0.00234 (15609) covalent geometry : angle 0.46060 (20932) *********************** 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 168 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8265 (mt) cc_final: 0.7921 (mp) REVERT: B 44 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8076 (ttp-170) REVERT: B 61 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8578 (mtpt) REVERT: B 69 GLU cc_start: 0.7568 (pp20) cc_final: 0.7314 (pp20) REVERT: B 102 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 152 MET cc_start: 0.8979 (mtm) cc_final: 0.8738 (mtp) REVERT: B 165 GLN cc_start: 0.8154 (mt0) cc_final: 0.7923 (mt0) REVERT: C 61 LYS cc_start: 0.8354 (mmtm) cc_final: 0.8057 (mptt) REVERT: D 1 MET cc_start: 0.4245 (mtm) cc_final: 0.4035 (mtm) REVERT: D 130 GLU cc_start: 0.8071 (mp0) cc_final: 0.7230 (pm20) REVERT: E 65 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: E 72 LYS cc_start: 0.8386 (tptt) cc_final: 0.8100 (tttp) REVERT: F 1 MET cc_start: 0.5171 (OUTLIER) cc_final: 0.4423 (ttt) REVERT: F 4 ASN cc_start: 0.6281 (p0) cc_final: 0.6071 (t0) REVERT: G 164 MET cc_start: 0.2406 (ttm) cc_final: 0.2012 (ttp) REVERT: G 214 MET cc_start: 0.1489 (pmm) cc_final: 0.1096 (ttp) REVERT: G 244 MET cc_start: 0.0473 (mtt) cc_final: -0.0166 (tpp) outliers start: 14 outliers final: 4 residues processed: 162 average time/residue: 1.4977 time to fit residues: 265.9330 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 : 1.587 ------------------------------------------------------------------------------- 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 61 LYS Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 51 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 152 optimal weight: 0.0370 chunk 170 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 C 121 GLN C 165 GLN E 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.209358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122695 restraints weight = 24155.538| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.47 r_work: 0.3227 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1798 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= 0.127 Angle : 0.490 8.026 20940 Z= 0.255 Chirality : 0.038 0.236 2306 Planarity : 0.004 0.053 2566 Dihedral : 16.302 179.647 2655 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.11 % Allowed : 9.03 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.20), residues: 1807 helix: 3.69 (0.13), residues: 1261 sheet: -0.63 (0.73), residues: 46 loop : -0.09 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 84 HIS 0.005 0.001 HIS D 82 PHE 0.016 0.001 PHE A 181 TYR 0.018 0.001 TYR B 208 ARG 0.003 0.000 ARG G 223 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 1126) hydrogen bonds : angle 3.71926 ( 3327) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.55439 ( 8) covalent geometry : bond 0.00265 (15609) covalent geometry : angle 0.48968 (20932) *********************** 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 168 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8202 (mt) cc_final: 0.7878 (mp) REVERT: B 44 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8046 (ttp-170) REVERT: B 61 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8591 (mtpt) REVERT: B 69 GLU cc_start: 0.7563 (pp20) cc_final: 0.7294 (pp20) REVERT: B 102 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7118 (mm-30) REVERT: B 152 MET cc_start: 0.8993 (mtm) cc_final: 0.8741 (mtp) REVERT: B 165 GLN cc_start: 0.8041 (mt0) cc_final: 0.7774 (mt0) REVERT: B 173 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8300 (tm) REVERT: C 61 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8051 (mptt) REVERT: D 1 MET cc_start: 0.4178 (mtm) cc_final: 0.3969 (mtm) REVERT: D 130 GLU cc_start: 0.8135 (mp0) cc_final: 0.7183 (pm20) REVERT: E 65 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: E 72 LYS cc_start: 0.8363 (tptt) cc_final: 0.8028 (tttp) REVERT: F 1 MET cc_start: 0.5212 (OUTLIER) cc_final: 0.4372 (ttt) REVERT: F 4 ASN cc_start: 0.6224 (p0) cc_final: 0.5866 (t0) REVERT: F 122 LEU cc_start: 0.2359 (mm) cc_final: 0.2118 (pp) REVERT: G 164 MET cc_start: 0.2474 (ttm) cc_final: 0.2114 (ttp) REVERT: G 244 MET cc_start: 0.0356 (mtt) cc_final: -0.0303 (tpp) outliers start: 18 outliers final: 5 residues processed: 159 average time/residue: 1.5108 time to fit residues: 263.2459 Evaluate side-chains 156 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 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 51 GLN Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 C 121 GLN C 165 GLN 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 = 0.208518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124941 restraints weight = 15651.168| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.40 r_work: 0.3273 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1873 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= 0.141 Angle : 0.510 9.304 20940 Z= 0.266 Chirality : 0.039 0.239 2306 Planarity : 0.004 0.053 2566 Dihedral : 16.394 179.631 2655 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.05 % Allowed : 9.34 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.20), residues: 1807 helix: 3.58 (0.13), residues: 1267 sheet: -0.71 (0.73), residues: 46 loop : -0.19 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 84 HIS 0.005 0.001 HIS D 82 PHE 0.018 0.002 PHE A 181 TYR 0.021 0.002 TYR B 208 ARG 0.004 0.000 ARG G 223 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 1126) hydrogen bonds : angle 3.78753 ( 3327) SS BOND : bond 0.00166 ( 4) SS BOND : angle 0.56790 ( 8) covalent geometry : bond 0.00301 (15609) covalent geometry : angle 0.51038 (20932) *********************** 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 171 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8264 (mt) cc_final: 0.7954 (mp) REVERT: B 44 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7967 (ttp-170) REVERT: B 61 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8560 (mtpt) REVERT: B 69 GLU cc_start: 0.7548 (pp20) cc_final: 0.7301 (pp20) REVERT: B 102 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7284 (mm-30) REVERT: B 152 MET cc_start: 0.8973 (mtm) cc_final: 0.8713 (mtp) REVERT: B 173 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8374 (tm) REVERT: C 61 LYS cc_start: 0.8390 (mmtm) cc_final: 0.8109 (mptt) REVERT: D 130 GLU cc_start: 0.8085 (mp0) cc_final: 0.7108 (pm20) REVERT: E 65 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: E 72 LYS cc_start: 0.8345 (tptt) cc_final: 0.8044 (tttp) REVERT: F 1 MET cc_start: 0.5182 (OUTLIER) cc_final: 0.4358 (ttt) REVERT: F 4 ASN cc_start: 0.6371 (p0) cc_final: 0.6083 (t0) REVERT: F 122 LEU cc_start: 0.2234 (mm) cc_final: 0.2009 (pp) REVERT: G 164 MET cc_start: 0.2474 (ttm) cc_final: 0.2156 (ttp) REVERT: G 214 MET cc_start: 0.1158 (pmm) cc_final: 0.0851 (ttp) REVERT: G 244 MET cc_start: 0.0114 (mtt) cc_final: -0.0468 (tpp) outliers start: 17 outliers final: 7 residues processed: 162 average time/residue: 1.5353 time to fit residues: 272.7506 Evaluate side-chains 160 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 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 51 GLN 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 177 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 80 optimal weight: 0.0970 chunk 125 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 C 121 GLN C 165 GLN E 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.209048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123881 restraints weight = 19829.054| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.54 r_work: 0.3262 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 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 = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1942 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= 0.129 Angle : 0.501 9.338 20940 Z= 0.259 Chirality : 0.038 0.251 2306 Planarity : 0.004 0.053 2566 Dihedral : 16.245 179.777 2655 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.19), residues: 1807 helix: 3.66 (0.13), residues: 1260 sheet: -1.03 (0.87), residues: 36 loop : -0.08 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 84 HIS 0.005 0.001 HIS D 82 PHE 0.016 0.001 PHE A 181 TYR 0.020 0.001 TYR B 208 ARG 0.003 0.000 ARG G 223 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 1126) hydrogen bonds : angle 3.72717 ( 3327) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.56217 ( 8) covalent geometry : bond 0.00271 (15609) covalent geometry : angle 0.50103 (20932) *********************** 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 167 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8260 (mt) cc_final: 0.7944 (mp) REVERT: A 257 MET cc_start: 0.3384 (mtp) cc_final: 0.3064 (ttp) REVERT: B 44 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8038 (ttp-170) REVERT: B 61 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8563 (mtpt) REVERT: B 69 GLU cc_start: 0.7538 (pp20) cc_final: 0.7293 (pp20) REVERT: B 102 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7300 (mm-30) REVERT: B 152 MET cc_start: 0.8975 (mtm) cc_final: 0.8715 (mtp) REVERT: B 173 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8319 (tm) REVERT: C 61 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8110 (mptt) REVERT: D 130 GLU cc_start: 0.8084 (mp0) cc_final: 0.7170 (pm20) REVERT: E 65 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: E 72 LYS cc_start: 0.8347 (tptt) cc_final: 0.8043 (tttp) REVERT: F 1 MET cc_start: 0.5238 (OUTLIER) cc_final: 0.4399 (ttt) REVERT: F 4 ASN cc_start: 0.6357 (p0) cc_final: 0.6064 (t0) REVERT: G 51 GLN cc_start: 0.6679 (mt0) cc_final: 0.6231 (mt0) REVERT: G 164 MET cc_start: 0.2331 (ttm) cc_final: 0.2023 (ttp) REVERT: G 214 MET cc_start: 0.1159 (pmm) cc_final: 0.0827 (ttp) REVERT: G 244 MET cc_start: 0.0177 (mtt) cc_final: -0.0461 (tpp) outliers start: 17 outliers final: 8 residues processed: 159 average time/residue: 1.5903 time to fit residues: 276.9939 Evaluate side-chains 162 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 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 51 GLN Chi-restraints excluded: chain F residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 29 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 C 121 GLN C 165 GLN E 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.207693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121879 restraints weight = 22067.666| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.63 r_work: 0.3234 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1999 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= 0.142 Angle : 0.526 11.928 20940 Z= 0.271 Chirality : 0.039 0.255 2306 Planarity : 0.004 0.053 2566 Dihedral : 16.306 178.917 2655 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.87 % Allowed : 9.89 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.20), residues: 1807 helix: 3.54 (0.13), residues: 1266 sheet: -1.75 (0.96), residues: 26 loop : -0.12 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 84 HIS 0.005 0.001 HIS D 82 PHE 0.019 0.002 PHE A 181 TYR 0.025 0.002 TYR B 208 ARG 0.004 0.000 ARG G 223 Details of bonding type rmsd hydrogen bonds : bond 0.05180 ( 1126) hydrogen bonds : angle 3.80160 ( 3327) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.58932 ( 8) covalent geometry : bond 0.00305 (15609) covalent geometry : angle 0.52591 (20932) ********************** 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 162 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3355 (mtp) cc_final: 0.3032 (ttp) REVERT: B 44 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8029 (ttp-170) REVERT: B 61 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8541 (mtpt) REVERT: B 69 GLU cc_start: 0.7568 (pp20) cc_final: 0.7300 (pp20) REVERT: B 102 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7328 (mm-30) REVERT: B 152 MET cc_start: 0.8997 (mtm) cc_final: 0.8743 (mtp) REVERT: B 173 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8412 (tm) REVERT: C 61 LYS cc_start: 0.8459 (mmtm) cc_final: 0.8144 (mptt) REVERT: D 130 GLU cc_start: 0.8139 (mp0) cc_final: 0.7208 (pm20) REVERT: E 65 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: E 72 LYS cc_start: 0.8375 (tptt) cc_final: 0.8071 (tttp) REVERT: F 1 MET cc_start: 0.5256 (OUTLIER) cc_final: 0.4386 (ttt) REVERT: G 4 ASN cc_start: 0.7088 (t0) cc_final: 0.6791 (t0) REVERT: G 51 GLN cc_start: 0.6635 (mt0) cc_final: 0.5932 (mt0) REVERT: G 164 MET cc_start: 0.2315 (ttm) cc_final: 0.2015 (ttp) REVERT: G 214 MET cc_start: 0.1242 (pmm) cc_final: 0.0711 (ttp) REVERT: G 244 MET cc_start: 0.0096 (mtt) cc_final: -0.0526 (tpp) outliers start: 14 outliers final: 8 residues processed: 155 average time/residue: 1.5298 time to fit residues: 260.4552 Evaluate side-chains 160 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 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 51 GLN Chi-restraints excluded: chain F residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 157 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.208234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122953 restraints weight = 20669.952| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.57 r_work: 0.3244 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 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 = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15613 Z= 0.142 Angle : 0.521 10.256 20940 Z= 0.269 Chirality : 0.039 0.245 2306 Planarity : 0.004 0.053 2566 Dihedral : 16.323 178.392 2655 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.93 % Allowed : 9.77 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.19), residues: 1807 helix: 3.59 (0.13), residues: 1260 sheet: -1.76 (0.83), residues: 22 loop : -0.13 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 84 HIS 0.006 0.001 HIS D 82 PHE 0.019 0.002 PHE A 181 TYR 0.026 0.002 TYR B 208 ARG 0.004 0.000 ARG G 223 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 1126) hydrogen bonds : angle 3.78886 ( 3327) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.59639 ( 8) covalent geometry : bond 0.00306 (15609) covalent geometry : angle 0.52095 (20932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22398.27 seconds wall clock time: 386 minutes 6.09 seconds (23166.09 seconds total)