Starting phenix.real_space_refine on Sun Aug 24 00:50:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyh_18754/08_2025/8qyh_18754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyh_18754/08_2025/8qyh_18754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qyh_18754/08_2025/8qyh_18754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyh_18754/08_2025/8qyh_18754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qyh_18754/08_2025/8qyh_18754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyh_18754/08_2025/8qyh_18754.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 49 5.16 5 C 10082 2.51 5 N 2447 2.21 5 O 3332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15925 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2146 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Conformer: "B" Number of residues, atoms: 269, 2146 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} bond proxies already assigned to first conformer: 2184 Chain: "B" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2146 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain: "C" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2146 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain: "D" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2146 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain: "E" Number of atoms: 2153 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2146 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Conformer: "B" Number of residues, atoms: 269, 2146 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} bond proxies already assigned to first conformer: 2186 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: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 151 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 151 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 151 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 151 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 151 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 4.96, per 1000 atoms: 0.31 Number of scatterers: 15925 At special positions: 0 Unit cell: (82.368, 82.368, 233.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 15 15.00 O 3332 8.00 N 2447 7.00 C 10082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 86 " distance=2.03 Simple disulfide: pdb=" SG CYS F 165 " - pdb=" SG CYS F 240 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 86 " distance=2.03 Simple disulfide: pdb=" SG CYS G 165 " - pdb=" SG CYS G 240 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 518.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3516 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 7 sheets defined 77.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 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 76 Processing helix chain 'A' and resid 80 through 90 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 220 removed outlier: 3.785A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 269 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 59 removed outlier: 3.839A pdb=" N ILE B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 80 through 90 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 269 removed outlier: 3.789A 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 17 through 38 Processing helix chain 'C' and resid 38 through 59 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.754A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 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: 3.833A pdb=" N LEU C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 269 Processing helix chain 'D' and resid 2 through 13 removed outlier: 3.779A pdb=" N SER D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 38 Processing helix chain 'D' and resid 38 through 58 Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.651A pdb=" N TRP D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) 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 218 Processing helix chain 'D' and resid 223 through 269 removed outlier: 3.507A pdb=" N GLU D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 17 through 38 removed outlier: 3.509A pdb=" N VAL E 21 " --> pdb=" O TYR E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 58 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 80 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 removed outlier: 3.634A pdb=" N HIS E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 220 removed outlier: 3.720A pdb=" N LEU E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 269 Processing helix chain 'F' and resid 19 through 79 Processing helix chain 'F' and resid 107 through 127 removed outlier: 3.705A 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: 3.934A 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: 3.581A pdb=" N ARG F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 47 removed outlier: 3.812A 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 Processing helix chain 'G' and resid 127 through 133 Processing helix chain 'G' and resid 148 through 168 Processing helix chain 'G' and resid 172 through 177 removed outlier: 3.628A pdb=" N ASN G 177 " --> pdb=" O PRO G 173 " (cutoff:3.500A) 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 91 through 98 removed outlier: 3.620A pdb=" N ARG A 106 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU A 96 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 104 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU A 98 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 98 removed outlier: 3.682A pdb=" N ARG B 106 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU B 96 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE B 104 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU B 98 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.953A 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 98 removed outlier: 3.597A pdb=" N ARG C 106 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU C 96 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE C 104 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU C 98 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 98 removed outlier: 3.636A pdb=" N ARG D 106 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU D 96 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE D 104 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU D 98 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 5.023A 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: 3.669A pdb=" N ARG E 106 " --> pdb=" O GLN E 94 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU E 96 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE E 104 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU E 98 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.996A 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: 5.248A pdb=" N PHE F 93 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL F 210 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU F 211 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 138 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN F 215 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN F 136 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N SER F 196 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 5.778A 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: 3.506A pdb=" N VAL G 83 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU G 211 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN G 215 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN G 136 " --> pdb=" O GLN G 215 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N LEU G 191 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE G 137 " --> pdb=" O LEU G 191 " (cutoff:3.500A) 1137 hydrogen bonds defined for protein. 3366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2427 1.30 - 1.43: 3971 1.43 - 1.56: 9172 1.56 - 1.69: 80 1.69 - 1.82: 89 Bond restraints: 15739 Sorted by residual: bond pdb=" C38 PEE E 302 " pdb=" C39 PEE E 302 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C38 PEE D 302 " pdb=" C39 PEE D 302 " ideal model delta sigma weight residual 1.523 1.297 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C38 PEE C 302 " pdb=" C39 PEE C 302 " ideal model delta sigma weight residual 1.523 1.297 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C18 PEE D 302 " pdb=" C19 PEE D 302 " ideal model delta sigma weight residual 1.523 1.298 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C18 PEE E 302 " pdb=" C19 PEE E 302 " ideal model delta sigma weight residual 1.523 1.300 0.223 2.00e-02 2.50e+03 1.25e+02 ... (remaining 15734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.36: 21086 10.36 - 20.72: 17 20.72 - 31.08: 0 31.08 - 41.44: 0 41.44 - 51.80: 4 Bond angle restraints: 21107 Sorted by residual: angle pdb=" C38 PEE B 302 " pdb=" C39 PEE B 302 " pdb=" C40 PEE B 302 " ideal model delta sigma weight residual 112.47 164.27 -51.80 3.00e+00 1.11e-01 2.98e+02 angle pdb=" C38 PEE A 302 " pdb=" C39 PEE A 302 " pdb=" C40 PEE A 302 " ideal model delta sigma weight residual 112.47 164.14 -51.67 3.00e+00 1.11e-01 2.97e+02 angle pdb=" C37 PEE B 302 " pdb=" C38 PEE B 302 " pdb=" C39 PEE B 302 " ideal model delta sigma weight residual 114.27 163.94 -49.67 3.00e+00 1.11e-01 2.74e+02 angle pdb=" C37 PEE A 302 " pdb=" C38 PEE A 302 " pdb=" C39 PEE A 302 " ideal model delta sigma weight residual 114.27 163.77 -49.50 3.00e+00 1.11e-01 2.72e+02 angle pdb=" N VAL C 23 " pdb=" CA VAL C 23 " pdb=" C VAL C 23 " ideal model delta sigma weight residual 110.62 104.76 5.86 1.02e+00 9.61e-01 3.30e+01 ... (remaining 21102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 9373 35.74 - 71.47: 306 71.47 - 107.21: 27 107.21 - 142.94: 7 142.94 - 178.68: 9 Dihedral angle restraints: 9722 sinusoidal: 4311 harmonic: 5411 Sorted by residual: dihedral pdb=" C4 PEE D 302 " pdb=" O4P PEE D 302 " pdb=" P PEE D 302 " pdb=" O3P PEE D 302 " ideal model delta sinusoidal sigma weight residual 171.78 -9.54 -178.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 PEE B 302 " pdb=" O4P PEE B 302 " pdb=" P PEE B 302 " pdb=" O3P PEE B 302 " ideal model delta sinusoidal sigma weight residual 171.78 1.85 169.93 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C32 PEE D 302 " pdb=" C30 PEE D 302 " pdb=" C31 PEE D 302 " pdb=" O3 PEE D 302 " ideal model delta sinusoidal sigma weight residual 161.16 -31.54 -167.30 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 9719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2291 0.110 - 0.221: 36 0.221 - 0.331: 1 0.331 - 0.441: 0 0.441 - 0.551: 3 Chirality restraints: 2331 Sorted by residual: chirality pdb=" C2 PEE B 302 " pdb=" C1 PEE B 302 " pdb=" C3 PEE B 302 " pdb=" O2 PEE B 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.88 0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" C2 PEE A 302 " pdb=" C1 PEE A 302 " pdb=" C3 PEE A 302 " pdb=" O2 PEE A 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.86 0.53 2.00e-01 2.50e+01 7.14e+00 chirality pdb=" CB VAL E 14 " pdb=" CA VAL E 14 " pdb=" CG1 VAL E 14 " pdb=" CG2 VAL E 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 2328 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 63 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO E 64 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 148 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C PHE E 148 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE E 148 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR E 149 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 65 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C GLU A 65 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU A 65 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 66 " 0.012 2.00e-02 2.50e+03 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 680 2.72 - 3.27: 16006 3.27 - 3.81: 28492 3.81 - 4.36: 34480 4.36 - 4.90: 57948 Nonbonded interactions: 137606 Sorted by model distance: nonbonded pdb=" NH2 ARG F 60 " pdb=" O PHE F 217 " model vdw 2.177 3.120 nonbonded pdb=" OH TYR E 208 " pdb=" OA4 CDL E 301 " model vdw 2.183 3.040 nonbonded pdb=" OD2 ASP E 217 " pdb=" O HOH E 401 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR F 143 " pdb=" OG SER F 156 " model vdw 2.205 3.040 nonbonded pdb=" O PHE C 132 " pdb=" O HOH C 401 " model vdw 2.212 3.040 ... (remaining 137601 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 302)) selection = (chain 'B' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 302)) selection = (chain 'C' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 302)) selection = (chain 'D' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 302)) selection = (chain 'E' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 302)) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.390 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 0.230 15743 Z= 0.425 Angle : 1.025 51.795 21115 Z= 0.444 Chirality : 0.044 0.551 2331 Planarity : 0.004 0.059 2586 Dihedral : 17.932 178.680 6194 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.12 % Allowed : 0.49 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.24 (0.20), residues: 1827 helix: 3.16 (0.14), residues: 1254 sheet: -0.32 (0.75), residues: 50 loop : -0.22 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.016 0.001 TYR E 208 PHE 0.015 0.001 PHE A 212 TRP 0.018 0.002 TRP A 84 HIS 0.003 0.000 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00798 (15739) covalent geometry : angle 1.02547 (21107) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.63974 ( 8) hydrogen bonds : bond 0.11211 ( 1137) hydrogen bonds : angle 4.65482 ( 3366) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8295 (mtt90) cc_final: 0.8001 (mtm110) REVERT: A 103 LYS cc_start: 0.7584 (ptmm) cc_final: 0.7250 (pttt) REVERT: A 121 GLN cc_start: 0.8421 (tt0) cc_final: 0.8073 (tt0) REVERT: B 60 GLU cc_start: 0.7545 (tp30) cc_final: 0.7303 (tm-30) REVERT: C 130 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8166 (mm-30) REVERT: C 159 ASP cc_start: 0.8522 (t0) cc_final: 0.8254 (t0) REVERT: E 15 GLU cc_start: 0.8098 (mp0) cc_final: 0.7759 (mp0) REVERT: E 81 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7868 (ttpt) REVERT: G 11 ARG cc_start: 0.5226 (ptp90) cc_final: 0.4610 (ptt180) REVERT: G 12 ARG cc_start: 0.3525 (tpp-160) cc_final: 0.2441 (mtm110) outliers start: 2 outliers final: 2 residues processed: 175 average time/residue: 0.6073 time to fit residues: 116.3706 Evaluate side-chains 140 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain E residue 14 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 76 GLN B 265 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 156 ASN C 265 GLN D 156 ASN D 265 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.199560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121726 restraints weight = 27271.886| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.98 r_work: 0.3309 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 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 = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15743 Z= 0.129 Angle : 0.492 8.864 21115 Z= 0.254 Chirality : 0.037 0.168 2331 Planarity : 0.004 0.050 2586 Dihedral : 18.848 174.925 2677 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.68 % Allowed : 5.29 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.51 (0.20), residues: 1827 helix: 3.45 (0.13), residues: 1253 sheet: -0.34 (0.75), residues: 49 loop : -0.38 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 70 TYR 0.023 0.001 TYR G 149 PHE 0.013 0.001 PHE A 212 TRP 0.014 0.001 TRP D 84 HIS 0.003 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00279 (15739) covalent geometry : angle 0.49243 (21107) SS BOND : bond 0.00123 ( 4) SS BOND : angle 0.46946 ( 8) hydrogen bonds : bond 0.04713 ( 1137) hydrogen bonds : angle 3.82522 ( 3366) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8552 (mtt90) cc_final: 0.8313 (mtm110) REVERT: A 103 LYS cc_start: 0.7668 (ptmm) cc_final: 0.7235 (pttt) REVERT: B 1 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6429 (mpp) REVERT: B 15 GLU cc_start: 0.8682 (mp0) cc_final: 0.8455 (mp0) REVERT: B 60 GLU cc_start: 0.7816 (tp30) cc_final: 0.7578 (tm-30) REVERT: D 175 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7925 (tpt170) REVERT: E 15 GLU cc_start: 0.8247 (mp0) cc_final: 0.7903 (mp0) REVERT: E 81 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8106 (ttpt) REVERT: G 12 ARG cc_start: 0.3286 (tpp-160) cc_final: 0.2185 (mtm110) REVERT: G 15 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5112 (tm-30) outliers start: 11 outliers final: 4 residues processed: 154 average time/residue: 0.6662 time to fit residues: 111.8615 Evaluate side-chains 143 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain G residue 15 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 121 GLN B 76 GLN B 121 GLN C 120 GLN D 5 ASN D 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.198772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121529 restraints weight = 22948.126| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.84 r_work: 0.3306 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15743 Z= 0.139 Angle : 0.480 11.191 21115 Z= 0.249 Chirality : 0.038 0.296 2331 Planarity : 0.004 0.045 2586 Dihedral : 17.751 160.404 2677 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.04 % Allowed : 6.82 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.52 (0.20), residues: 1827 helix: 3.47 (0.13), residues: 1259 sheet: -0.45 (0.74), residues: 51 loop : -0.41 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 70 TYR 0.021 0.001 TYR E 208 PHE 0.013 0.001 PHE G 20 TRP 0.014 0.001 TRP D 84 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00316 (15739) covalent geometry : angle 0.47957 (21107) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.44605 ( 8) hydrogen bonds : bond 0.04733 ( 1137) hydrogen bonds : angle 3.71985 ( 3366) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8589 (mtt90) cc_final: 0.8282 (mtm110) REVERT: A 103 LYS cc_start: 0.7686 (ptmm) cc_final: 0.7291 (pttt) REVERT: B 15 GLU cc_start: 0.8686 (mp0) cc_final: 0.8447 (mp0) REVERT: B 60 GLU cc_start: 0.7785 (tp30) cc_final: 0.7558 (tm-30) REVERT: D 12 THR cc_start: 0.7811 (m) cc_final: 0.7157 (p) REVERT: D 156 ASN cc_start: 0.8629 (m110) cc_final: 0.8397 (m110) REVERT: D 175 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7839 (tpt170) REVERT: D 238 GLU cc_start: 0.6696 (pt0) cc_final: 0.6397 (mp0) REVERT: E 15 GLU cc_start: 0.8218 (mp0) cc_final: 0.7882 (mp0) REVERT: E 81 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8107 (ttpt) REVERT: E 182 LEU cc_start: 0.8592 (tp) cc_final: 0.8168 (mm) REVERT: F 214 MET cc_start: 0.5118 (mpp) cc_final: 0.4318 (mmm) REVERT: G 12 ARG cc_start: 0.3356 (tpp-160) cc_final: 0.2270 (mtm110) REVERT: G 15 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5168 (tm-30) outliers start: 17 outliers final: 6 residues processed: 158 average time/residue: 0.6847 time to fit residues: 118.4926 Evaluate side-chains 149 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain G residue 15 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 chunk 162 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 137 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 121 GLN B 76 GLN B 121 GLN C 120 GLN E 76 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.199343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121513 restraints weight = 27780.889| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.00 r_work: 0.3301 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 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 = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15743 Z= 0.121 Angle : 0.458 14.200 21115 Z= 0.237 Chirality : 0.037 0.229 2331 Planarity : 0.003 0.044 2586 Dihedral : 17.041 154.679 2676 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.92 % Allowed : 7.68 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.68 (0.20), residues: 1827 helix: 3.59 (0.13), residues: 1252 sheet: -0.29 (0.77), residues: 51 loop : -0.34 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 11 TYR 0.020 0.001 TYR E 208 PHE 0.013 0.001 PHE A 212 TRP 0.013 0.001 TRP D 84 HIS 0.002 0.000 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00268 (15739) covalent geometry : angle 0.45806 (21107) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.39433 ( 8) hydrogen bonds : bond 0.04473 ( 1137) hydrogen bonds : angle 3.61108 ( 3366) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8610 (mtt90) cc_final: 0.8329 (mtm110) REVERT: A 103 LYS cc_start: 0.7698 (ptmm) cc_final: 0.7330 (pttt) REVERT: B 15 GLU cc_start: 0.8688 (mp0) cc_final: 0.8478 (mp0) REVERT: B 60 GLU cc_start: 0.7839 (tp30) cc_final: 0.7615 (tm-30) REVERT: D 130 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: D 156 ASN cc_start: 0.8589 (m110) cc_final: 0.8380 (m-40) REVERT: D 159 ASP cc_start: 0.8351 (t0) cc_final: 0.8103 (t70) REVERT: D 175 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7797 (tpt170) REVERT: D 238 GLU cc_start: 0.6759 (pt0) cc_final: 0.6488 (mp0) REVERT: E 15 GLU cc_start: 0.8270 (mp0) cc_final: 0.7928 (mp0) REVERT: E 81 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8056 (ttpt) REVERT: F 98 ARG cc_start: 0.3923 (mtt-85) cc_final: 0.2970 (tpp80) REVERT: F 164 MET cc_start: 0.0327 (tmt) cc_final: -0.0612 (ptp) REVERT: F 214 MET cc_start: 0.5138 (mpp) cc_final: 0.4370 (mmm) REVERT: G 12 ARG cc_start: 0.3379 (tpp-160) cc_final: 0.2292 (mtm110) REVERT: G 15 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5149 (tm-30) REVERT: G 214 MET cc_start: 0.3757 (ptt) cc_final: 0.3512 (ptm) outliers start: 15 outliers final: 7 residues processed: 160 average time/residue: 0.7163 time to fit residues: 125.1088 Evaluate side-chains 155 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 163 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 0.0030 chunk 154 optimal weight: 0.0030 chunk 169 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 76 GLN B 121 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.200490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123062 restraints weight = 27350.754| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.99 r_work: 0.3326 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 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 = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 15743 Z= 0.104 Angle : 0.439 12.465 21115 Z= 0.227 Chirality : 0.036 0.201 2331 Planarity : 0.003 0.044 2586 Dihedral : 16.569 153.053 2676 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.17 % Allowed : 8.48 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.20), residues: 1827 helix: 3.71 (0.13), residues: 1252 sheet: -0.53 (0.78), residues: 49 loop : -0.31 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 159 TYR 0.017 0.001 TYR E 208 PHE 0.013 0.001 PHE A 212 TRP 0.013 0.001 TRP A 84 HIS 0.002 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00215 (15739) covalent geometry : angle 0.43945 (21107) SS BOND : bond 0.00066 ( 4) SS BOND : angle 0.34480 ( 8) hydrogen bonds : bond 0.04219 ( 1137) hydrogen bonds : angle 3.52646 ( 3366) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8560 (mtt90) cc_final: 0.8289 (mtm110) REVERT: A 103 LYS cc_start: 0.7702 (ptmm) cc_final: 0.6864 (ttmm) REVERT: B 15 GLU cc_start: 0.8675 (mp0) cc_final: 0.8462 (mp0) REVERT: B 60 GLU cc_start: 0.7776 (tp30) cc_final: 0.7548 (tm-30) REVERT: D 12 THR cc_start: 0.7743 (m) cc_final: 0.7116 (p) REVERT: D 79 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: D 130 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: D 159 ASP cc_start: 0.8301 (t0) cc_final: 0.8082 (t70) REVERT: D 175 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7756 (tpt170) REVERT: E 15 GLU cc_start: 0.8265 (mp0) cc_final: 0.7915 (mp0) REVERT: E 81 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7994 (ttpt) REVERT: F 98 ARG cc_start: 0.3883 (mtt-85) cc_final: 0.2905 (tpp80) REVERT: F 164 MET cc_start: 0.0203 (tmt) cc_final: -0.0705 (ptp) REVERT: F 214 MET cc_start: 0.5116 (OUTLIER) cc_final: 0.4375 (mmm) REVERT: G 12 ARG cc_start: 0.3291 (tpp-160) cc_final: 0.2225 (mtm110) REVERT: G 15 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5101 (tm-30) REVERT: G 214 MET cc_start: 0.3854 (ptt) cc_final: 0.3573 (ptm) outliers start: 19 outliers final: 6 residues processed: 156 average time/residue: 0.5637 time to fit residues: 96.3661 Evaluate side-chains 153 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 50 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 76 GLN B 121 GLN C 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121208 restraints weight = 30305.394| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.59 r_work: 0.3267 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15743 Z= 0.133 Angle : 0.466 11.399 21115 Z= 0.242 Chirality : 0.038 0.192 2331 Planarity : 0.003 0.043 2586 Dihedral : 16.389 152.988 2676 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.29 % Allowed : 9.10 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.69 (0.19), residues: 1827 helix: 3.61 (0.13), residues: 1259 sheet: -0.33 (0.76), residues: 51 loop : -0.40 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.021 0.001 TYR E 208 PHE 0.013 0.001 PHE G 20 TRP 0.012 0.001 TRP D 84 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00302 (15739) covalent geometry : angle 0.46630 (21107) SS BOND : bond 0.00112 ( 4) SS BOND : angle 0.41878 ( 8) hydrogen bonds : bond 0.04568 ( 1137) hydrogen bonds : angle 3.57209 ( 3366) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8446 (mtt90) cc_final: 0.8178 (mtm110) REVERT: A 69 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: A 103 LYS cc_start: 0.7673 (ptmm) cc_final: 0.6865 (ttmm) REVERT: D 79 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: D 130 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: D 159 ASP cc_start: 0.8271 (t0) cc_final: 0.8050 (t70) REVERT: D 175 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7688 (tpt170) REVERT: E 15 GLU cc_start: 0.8138 (mp0) cc_final: 0.7808 (mp0) REVERT: E 81 LYS cc_start: 0.8272 (ttpp) cc_final: 0.8034 (ttpt) REVERT: E 182 LEU cc_start: 0.8618 (tp) cc_final: 0.8186 (mm) REVERT: E 257 MET cc_start: 0.4701 (mtm) cc_final: 0.4399 (pmm) REVERT: F 98 ARG cc_start: 0.3912 (mtt-85) cc_final: 0.2857 (tpp80) REVERT: F 164 MET cc_start: 0.0155 (OUTLIER) cc_final: -0.0814 (ptp) REVERT: F 214 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4369 (mmm) REVERT: G 12 ARG cc_start: 0.3366 (tpp-160) cc_final: 0.2418 (mtm110) REVERT: G 15 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5128 (tm-30) REVERT: G 214 MET cc_start: 0.3783 (ptt) cc_final: 0.3487 (ptm) outliers start: 21 outliers final: 5 residues processed: 161 average time/residue: 0.5825 time to fit residues: 102.7927 Evaluate side-chains 154 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 158 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 76 GLN B 121 GLN C 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.198886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119358 restraints weight = 35818.129| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.89 r_work: 0.3240 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15743 Z= 0.134 Angle : 0.466 15.811 21115 Z= 0.241 Chirality : 0.037 0.180 2331 Planarity : 0.003 0.042 2586 Dihedral : 16.147 158.122 2676 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.11 % Allowed : 9.53 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.68 (0.19), residues: 1827 helix: 3.59 (0.13), residues: 1259 sheet: -0.51 (0.76), residues: 49 loop : -0.36 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 255 TYR 0.020 0.001 TYR E 208 PHE 0.013 0.001 PHE G 20 TRP 0.013 0.001 TRP D 84 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00305 (15739) covalent geometry : angle 0.46566 (21107) SS BOND : bond 0.00112 ( 4) SS BOND : angle 0.46115 ( 8) hydrogen bonds : bond 0.04587 ( 1137) hydrogen bonds : angle 3.57139 ( 3366) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8484 (mtt90) cc_final: 0.8199 (mtm110) REVERT: A 103 LYS cc_start: 0.7580 (ptmm) cc_final: 0.7001 (ttpp) REVERT: A 152 MET cc_start: 0.8328 (mtm) cc_final: 0.7986 (mtt) REVERT: D 12 THR cc_start: 0.7899 (m) cc_final: 0.7414 (p) REVERT: D 130 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: D 159 ASP cc_start: 0.8284 (t0) cc_final: 0.8042 (t70) REVERT: D 175 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7704 (tpt170) REVERT: E 15 GLU cc_start: 0.8175 (mp0) cc_final: 0.7849 (mp0) REVERT: E 81 LYS cc_start: 0.8294 (ttpp) cc_final: 0.8025 (ttpt) REVERT: E 182 LEU cc_start: 0.8558 (tp) cc_final: 0.8150 (mm) REVERT: E 257 MET cc_start: 0.4655 (mtm) cc_final: 0.4417 (pmm) REVERT: F 98 ARG cc_start: 0.3906 (mtt-85) cc_final: 0.2738 (tpp80) REVERT: F 164 MET cc_start: 0.0402 (OUTLIER) cc_final: 0.0130 (ttt) REVERT: F 214 MET cc_start: 0.5183 (OUTLIER) cc_final: 0.4374 (mmm) REVERT: G 12 ARG cc_start: 0.3377 (tpp-160) cc_final: 0.2416 (mtm110) REVERT: G 15 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.5122 (tm-30) REVERT: G 155 LEU cc_start: 0.3554 (tp) cc_final: 0.2569 (mp) REVERT: G 214 MET cc_start: 0.3788 (ptt) cc_final: 0.3502 (ptm) outliers start: 18 outliers final: 6 residues processed: 158 average time/residue: 0.6404 time to fit residues: 110.9327 Evaluate side-chains 156 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 58 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 175 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 76 GLN B 121 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.198997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121329 restraints weight = 31091.375| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.56 r_work: 0.3269 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15743 Z= 0.125 Angle : 0.456 13.928 21115 Z= 0.237 Chirality : 0.037 0.185 2331 Planarity : 0.003 0.042 2586 Dihedral : 15.881 160.532 2676 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.17 % Allowed : 9.65 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.72 (0.19), residues: 1827 helix: 3.62 (0.13), residues: 1259 sheet: -0.26 (0.74), residues: 51 loop : -0.37 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 255 TYR 0.019 0.001 TYR E 208 PHE 0.012 0.001 PHE A 212 TRP 0.013 0.001 TRP D 84 HIS 0.002 0.000 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00282 (15739) covalent geometry : angle 0.45579 (21107) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.40807 ( 8) hydrogen bonds : bond 0.04489 ( 1137) hydrogen bonds : angle 3.54574 ( 3366) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8455 (mtt90) cc_final: 0.8172 (mtm110) REVERT: A 103 LYS cc_start: 0.7567 (ptmm) cc_final: 0.6996 (ttpp) REVERT: A 121 GLN cc_start: 0.8489 (tt0) cc_final: 0.8263 (mt0) REVERT: A 152 MET cc_start: 0.8366 (mtm) cc_final: 0.8003 (mtt) REVERT: B 175 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7298 (tpp-160) REVERT: D 130 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: D 159 ASP cc_start: 0.8257 (t0) cc_final: 0.8025 (t70) REVERT: D 175 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7674 (tpt170) REVERT: E 15 GLU cc_start: 0.8167 (mp0) cc_final: 0.7854 (mp0) REVERT: E 81 LYS cc_start: 0.8291 (ttpp) cc_final: 0.8040 (ttpt) REVERT: E 182 LEU cc_start: 0.8580 (tp) cc_final: 0.8184 (mm) REVERT: E 257 MET cc_start: 0.4870 (mtm) cc_final: 0.4666 (ptp) REVERT: F 98 ARG cc_start: 0.3945 (mtt-85) cc_final: 0.2672 (tpp80) REVERT: F 164 MET cc_start: 0.0431 (OUTLIER) cc_final: 0.0117 (ttt) REVERT: F 214 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4357 (mmm) REVERT: G 12 ARG cc_start: 0.3391 (tpp-160) cc_final: 0.2455 (mtm110) REVERT: G 15 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5088 (tm-30) REVERT: G 155 LEU cc_start: 0.3633 (tp) cc_final: 0.2581 (mp) REVERT: G 214 MET cc_start: 0.3696 (ptt) cc_final: 0.3433 (ptm) outliers start: 19 outliers final: 6 residues processed: 161 average time/residue: 0.6294 time to fit residues: 110.8200 Evaluate side-chains 156 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain G residue 15 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 75 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 39 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 76 GLN B 121 GLN C 120 GLN E 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.197769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118589 restraints weight = 24742.001| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.95 r_work: 0.3244 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15743 Z= 0.149 Angle : 0.485 13.558 21115 Z= 0.252 Chirality : 0.038 0.188 2331 Planarity : 0.004 0.043 2586 Dihedral : 15.898 160.369 2676 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.17 % Allowed : 10.14 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.64 (0.19), residues: 1827 helix: 3.54 (0.13), residues: 1260 sheet: -0.15 (0.74), residues: 51 loop : -0.35 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 49 TYR 0.022 0.001 TYR E 208 PHE 0.015 0.001 PHE G 20 TRP 0.012 0.001 TRP D 84 HIS 0.004 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00347 (15739) covalent geometry : angle 0.48503 (21107) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.36501 ( 8) hydrogen bonds : bond 0.04766 ( 1137) hydrogen bonds : angle 3.60357 ( 3366) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8321 (mtm110) REVERT: A 103 LYS cc_start: 0.7639 (ptmm) cc_final: 0.7031 (ttpp) REVERT: A 121 GLN cc_start: 0.8660 (tt0) cc_final: 0.8394 (mt0) REVERT: A 151 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8352 (mm) REVERT: A 152 MET cc_start: 0.8536 (mtm) cc_final: 0.8311 (mtt) REVERT: B 175 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7508 (tpp-160) REVERT: D 12 THR cc_start: 0.7975 (m) cc_final: 0.7548 (p) REVERT: D 130 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: D 159 ASP cc_start: 0.8351 (t0) cc_final: 0.8088 (t70) REVERT: D 175 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7818 (tpt170) REVERT: E 15 GLU cc_start: 0.8257 (mp0) cc_final: 0.7924 (mp0) REVERT: E 81 LYS cc_start: 0.8349 (ttpp) cc_final: 0.8069 (ttpt) REVERT: E 182 LEU cc_start: 0.8677 (tp) cc_final: 0.8261 (mm) REVERT: E 257 MET cc_start: 0.4985 (mtm) cc_final: 0.4766 (ptp) REVERT: F 98 ARG cc_start: 0.3907 (mtt-85) cc_final: 0.2685 (tpp80) REVERT: F 164 MET cc_start: 0.0448 (OUTLIER) cc_final: 0.0185 (ttt) REVERT: F 214 MET cc_start: 0.5064 (mpp) cc_final: 0.4247 (mmm) REVERT: G 12 ARG cc_start: 0.3343 (tpp-160) cc_final: 0.2280 (mtm180) REVERT: G 15 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5129 (tm-30) REVERT: G 155 LEU cc_start: 0.3528 (tp) cc_final: 0.2604 (mp) REVERT: G 214 MET cc_start: 0.3879 (ptt) cc_final: 0.3669 (ptm) outliers start: 19 outliers final: 7 residues processed: 159 average time/residue: 0.6314 time to fit residues: 110.3145 Evaluate side-chains 157 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain G residue 15 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 114 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 105 optimal weight: 0.4980 chunk 153 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 164 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 76 GLN B 121 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.198868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119089 restraints weight = 31353.239| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.13 r_work: 0.3240 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15743 Z= 0.118 Angle : 0.454 13.431 21115 Z= 0.236 Chirality : 0.037 0.194 2331 Planarity : 0.003 0.042 2586 Dihedral : 15.609 161.728 2676 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.11 % Allowed : 10.33 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.77 (0.19), residues: 1827 helix: 3.65 (0.13), residues: 1259 sheet: -0.28 (0.76), residues: 49 loop : -0.29 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 11 TYR 0.018 0.001 TYR E 208 PHE 0.012 0.001 PHE A 212 TRP 0.014 0.001 TRP D 84 HIS 0.002 0.000 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00260 (15739) covalent geometry : angle 0.45430 (21107) SS BOND : bond 0.00100 ( 4) SS BOND : angle 0.36875 ( 8) hydrogen bonds : bond 0.04407 ( 1137) hydrogen bonds : angle 3.52282 ( 3366) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8371 (mtm110) REVERT: A 103 LYS cc_start: 0.7590 (ptmm) cc_final: 0.6993 (ttpp) REVERT: A 121 GLN cc_start: 0.8657 (tt0) cc_final: 0.8380 (mt0) REVERT: A 151 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8332 (mm) REVERT: A 152 MET cc_start: 0.8466 (mtm) cc_final: 0.8159 (mtt) REVERT: D 12 THR cc_start: 0.7892 (m) cc_final: 0.7427 (p) REVERT: D 159 ASP cc_start: 0.8359 (t0) cc_final: 0.8112 (t70) REVERT: D 175 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7778 (tpt170) REVERT: E 15 GLU cc_start: 0.8317 (mp0) cc_final: 0.7968 (mp0) REVERT: E 81 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8086 (ttpt) REVERT: E 182 LEU cc_start: 0.8649 (tp) cc_final: 0.8237 (mm) REVERT: E 257 MET cc_start: 0.4891 (mtm) cc_final: 0.4687 (ptp) REVERT: F 98 ARG cc_start: 0.3928 (mtt-85) cc_final: 0.2701 (tpp80) REVERT: F 164 MET cc_start: 0.0555 (OUTLIER) cc_final: 0.0297 (ttt) REVERT: F 212 LEU cc_start: 0.2097 (OUTLIER) cc_final: 0.1535 (mt) REVERT: F 214 MET cc_start: 0.5215 (mpp) cc_final: 0.4346 (mmm) REVERT: G 12 ARG cc_start: 0.3258 (tpp-160) cc_final: 0.2144 (mtm180) REVERT: G 15 GLU cc_start: 0.5917 (OUTLIER) cc_final: 0.5056 (tm-30) REVERT: G 70 ARG cc_start: 0.2517 (ttp-110) cc_final: 0.1857 (tmm-80) REVERT: G 155 LEU cc_start: 0.3439 (tp) cc_final: 0.2516 (mp) REVERT: G 214 MET cc_start: 0.4037 (ptt) cc_final: 0.3825 (ptm) outliers start: 18 outliers final: 8 residues processed: 160 average time/residue: 0.6373 time to fit residues: 111.6810 Evaluate side-chains 158 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 15 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 157 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 76 GLN B 121 GLN C 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.198136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117731 restraints weight = 27987.825| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.52 r_work: 0.3242 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15743 Z= 0.132 Angle : 0.471 13.039 21115 Z= 0.244 Chirality : 0.038 0.195 2331 Planarity : 0.004 0.064 2586 Dihedral : 15.567 161.811 2676 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.11 % Allowed : 10.45 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.70 (0.19), residues: 1827 helix: 3.59 (0.13), residues: 1259 sheet: -0.02 (0.74), residues: 51 loop : -0.37 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.020 0.001 TYR E 208 PHE 0.013 0.001 PHE G 20 TRP 0.013 0.001 TRP D 84 HIS 0.003 0.000 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00300 (15739) covalent geometry : angle 0.47155 (21107) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.29134 ( 8) hydrogen bonds : bond 0.04567 ( 1137) hydrogen bonds : angle 3.55457 ( 3366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7564.34 seconds wall clock time: 129 minutes 10.12 seconds (7750.12 seconds total)