Starting phenix.real_space_refine on Sat Jun 14 05:40:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyh_18754/06_2025/8qyh_18754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyh_18754/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyh_18754/06_2025/8qyh_18754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyh_18754/06_2025/8qyh_18754.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyh_18754/06_2025/8qyh_18754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyh_18754/06_2025/8qyh_18754.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.084 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.75, per 1000 atoms: 0.93 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: 3.92 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 17 through 38 Processing helix chain 'A' and resid 38 through 58 Processing helix chain 'A' and resid 63 through 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: 4.96 Time building geometry restraints manager: 4.63 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 269 or resid 301 through 302)) selection = (chain 'B' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 269 or resid 301 through 302)) selection = (chain 'C' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 269 or resid 301 through 302)) selection = (chain 'D' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 269 or resid 301 through 302)) selection = (chain 'E' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 269 or resid 301 through 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: 8.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.170 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.400 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (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 TRP 0.018 0.002 TRP A 84 HIS 0.003 0.000 HIS A 70 PHE 0.015 0.001 PHE A 212 TYR 0.016 0.001 TYR E 208 ARG 0.003 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.11211 ( 1137) hydrogen bonds : angle 4.65482 ( 3366) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.63974 ( 8) covalent geometry : bond 0.00798 (15739) covalent geometry : angle 1.02547 (21107) *********************** 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 : 1.702 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: 1.4095 time to fit residues: 270.8926 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 : 1.543 ------------------------------------------------------------------------------- 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 150 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 139 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.198121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120174 restraints weight = 24614.389| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.88 r_work: 0.3283 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 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 = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15743 Z= 0.167 Angle : 0.526 8.627 21115 Z= 0.272 Chirality : 0.039 0.169 2331 Planarity : 0.004 0.049 2586 Dihedral : 18.978 173.768 2677 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.80 % Allowed : 5.53 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.19), residues: 1827 helix: 3.31 (0.13), residues: 1256 sheet: -0.37 (0.74), residues: 49 loop : -0.51 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 84 HIS 0.004 0.001 HIS E 134 PHE 0.015 0.002 PHE G 20 TYR 0.023 0.002 TYR E 208 ARG 0.006 0.001 ARG G 70 Details of bonding type rmsd hydrogen bonds : bond 0.05099 ( 1137) hydrogen bonds : angle 3.89562 ( 3366) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.47631 ( 8) covalent geometry : bond 0.00388 (15739) covalent geometry : angle 0.52587 (21107) *********************** 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: 13 poor density : 146 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8557 (mtt90) cc_final: 0.8264 (mtm110) REVERT: A 103 LYS cc_start: 0.7678 (ptmm) cc_final: 0.7261 (pttt) REVERT: B 15 GLU cc_start: 0.8670 (mp0) cc_final: 0.8447 (mp0) REVERT: B 60 GLU cc_start: 0.7786 (tp30) cc_final: 0.7572 (tm-30) REVERT: D 175 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7924 (tpt170) REVERT: E 15 GLU cc_start: 0.8238 (mp0) cc_final: 0.7886 (mp0) REVERT: E 81 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8131 (ttpt) REVERT: G 12 ARG cc_start: 0.3394 (tpp-160) cc_final: 0.2263 (mtm110) REVERT: G 15 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5217 (tm-30) outliers start: 13 outliers final: 8 residues processed: 153 average time/residue: 1.4037 time to fit residues: 236.1431 Evaluate side-chains 144 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER 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 96 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 50 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 100 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN F 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121139 restraints weight = 29327.710| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.54 r_work: 0.3256 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 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 = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1154 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= 0.138 Angle : 0.481 12.172 21115 Z= 0.249 Chirality : 0.038 0.279 2331 Planarity : 0.004 0.044 2586 Dihedral : 17.878 163.428 2677 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.23 % Allowed : 7.13 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.19), residues: 1827 helix: 3.43 (0.13), residues: 1259 sheet: -0.52 (0.74), residues: 51 loop : -0.42 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 84 HIS 0.003 0.001 HIS A 70 PHE 0.013 0.001 PHE A 212 TYR 0.021 0.001 TYR E 208 ARG 0.004 0.000 ARG G 159 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 1137) hydrogen bonds : angle 3.72769 ( 3366) SS BOND : bond 0.00089 ( 4) SS BOND : angle 0.41363 ( 8) covalent geometry : bond 0.00313 (15739) covalent geometry : angle 0.48076 (21107) *********************** 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 166 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8649 (mtt90) cc_final: 0.8336 (mtm110) REVERT: A 103 LYS cc_start: 0.7691 (ptmm) cc_final: 0.7304 (pttt) REVERT: B 15 GLU cc_start: 0.8708 (mp0) cc_final: 0.8477 (mp0) REVERT: B 60 GLU cc_start: 0.7869 (tp30) cc_final: 0.7627 (tm-30) REVERT: B 175 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7563 (tpp-160) REVERT: D 156 ASN cc_start: 0.8628 (m110) cc_final: 0.8418 (m110) REVERT: D 175 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7898 (tpt170) REVERT: E 15 GLU cc_start: 0.8256 (mp0) cc_final: 0.7916 (mp0) REVERT: E 81 LYS cc_start: 0.8372 (ttpp) cc_final: 0.8116 (ttpt) REVERT: E 182 LEU cc_start: 0.8632 (tp) cc_final: 0.8176 (mm) REVERT: F 214 MET cc_start: 0.5262 (mpp) cc_final: 0.4447 (mmm) REVERT: G 12 ARG cc_start: 0.3321 (tpp-160) cc_final: 0.2169 (mtm180) REVERT: G 15 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5213 (tm-30) outliers start: 20 outliers final: 7 residues processed: 158 average time/residue: 1.4893 time to fit residues: 258.2405 Evaluate side-chains 149 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 B residue 175 ARG 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 Chi-restraints excluded: chain G residue 50 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 167 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 121 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120367 restraints weight = 28432.296| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.01 r_work: 0.3286 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 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 = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1338 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 : 0.473 13.923 21115 Z= 0.244 Chirality : 0.038 0.212 2331 Planarity : 0.003 0.042 2586 Dihedral : 17.136 157.159 2676 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.04 % Allowed : 8.24 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.19), residues: 1827 helix: 3.51 (0.13), residues: 1260 sheet: -0.38 (0.76), residues: 51 loop : -0.32 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 84 HIS 0.002 0.000 HIS D 82 PHE 0.012 0.001 PHE A 212 TYR 0.020 0.001 TYR E 208 ARG 0.008 0.000 ARG G 159 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 1137) hydrogen bonds : angle 3.64510 ( 3366) SS BOND : bond 0.00105 ( 4) SS BOND : angle 0.40720 ( 8) covalent geometry : bond 0.00299 (15739) covalent geometry : angle 0.47272 (21107) *********************** 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 163 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8306 (mtm110) REVERT: A 103 LYS cc_start: 0.7728 (ptmm) cc_final: 0.6885 (ttmm) REVERT: B 60 GLU cc_start: 0.7824 (tp30) cc_final: 0.7600 (tm-30) REVERT: B 175 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7465 (tpp-160) REVERT: D 159 ASP cc_start: 0.8356 (t0) cc_final: 0.8106 (t70) REVERT: D 175 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7836 (tpt170) REVERT: E 15 GLU cc_start: 0.8275 (mp0) cc_final: 0.7924 (mp0) REVERT: E 81 LYS cc_start: 0.8354 (ttpp) cc_final: 0.8065 (ttpt) REVERT: F 164 MET cc_start: 0.0262 (tmt) cc_final: -0.0658 (ptp) REVERT: F 214 MET cc_start: 0.5006 (mpp) cc_final: 0.4325 (mmm) REVERT: G 11 ARG cc_start: 0.4727 (ptt-90) cc_final: 0.4355 (ptp90) REVERT: G 12 ARG cc_start: 0.3382 (tpp-160) cc_final: 0.2318 (mtm180) REVERT: G 15 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5150 (tm-30) REVERT: G 155 LEU cc_start: 0.3301 (tp) cc_final: 0.2356 (mp) outliers start: 17 outliers final: 8 residues processed: 156 average time/residue: 1.3423 time to fit residues: 231.2171 Evaluate side-chains 154 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 69 GLU Chi-restraints excluded: chain B residue 175 ARG 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 Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 214 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 170 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121025 restraints weight = 36636.515| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.02 r_work: 0.3239 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 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 = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1429 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= 0.124 Angle : 0.458 12.046 21115 Z= 0.237 Chirality : 0.037 0.201 2331 Planarity : 0.003 0.042 2586 Dihedral : 16.771 152.245 2676 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.29 % Allowed : 8.97 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.20), residues: 1827 helix: 3.57 (0.13), residues: 1259 sheet: -0.67 (0.78), residues: 49 loop : -0.37 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 84 HIS 0.002 0.000 HIS D 82 PHE 0.013 0.001 PHE A 212 TYR 0.020 0.001 TYR E 208 ARG 0.006 0.000 ARG G 159 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 1137) hydrogen bonds : angle 3.58890 ( 3366) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.40222 ( 8) covalent geometry : bond 0.00278 (15739) covalent geometry : angle 0.45772 (21107) *********************** 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 176 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8503 (mtt90) cc_final: 0.8240 (mtm110) REVERT: A 69 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 103 LYS cc_start: 0.7681 (ptmm) cc_final: 0.6846 (ttmm) REVERT: B 15 GLU cc_start: 0.8608 (mp0) cc_final: 0.8402 (mp0) REVERT: D 79 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: D 159 ASP cc_start: 0.8269 (t0) cc_final: 0.8048 (t70) REVERT: D 175 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7714 (tpt170) REVERT: E 15 GLU cc_start: 0.8174 (mp0) cc_final: 0.7833 (mp0) REVERT: E 81 LYS cc_start: 0.8315 (ttpp) cc_final: 0.8041 (ttpt) REVERT: F 164 MET cc_start: 0.0118 (OUTLIER) cc_final: -0.0868 (ptp) REVERT: F 214 MET cc_start: 0.4979 (OUTLIER) cc_final: 0.4511 (mmm) REVERT: G 12 ARG cc_start: 0.3369 (tpp-160) cc_final: 0.2353 (mtm180) REVERT: G 15 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5110 (tm-30) REVERT: G 155 LEU cc_start: 0.3266 (tp) cc_final: 0.2316 (mp) REVERT: G 214 MET cc_start: 0.3635 (ptt) cc_final: 0.3322 (ptm) outliers start: 21 outliers final: 6 residues processed: 169 average time/residue: 1.4172 time to fit residues: 263.4710 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 : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 79 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 119 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 E 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.196687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118550 restraints weight = 27257.423| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.98 r_work: 0.3252 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.092 | | 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) = 0.092 | | 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: 0.8520 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15743 Z= 0.188 Angle : 0.525 16.706 21115 Z= 0.271 Chirality : 0.040 0.178 2331 Planarity : 0.004 0.041 2586 Dihedral : 16.882 154.378 2676 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.17 % Allowed : 9.90 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.19), residues: 1827 helix: 3.38 (0.13), residues: 1260 sheet: -0.62 (0.76), residues: 51 loop : -0.36 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 84 HIS 0.004 0.001 HIS D 82 PHE 0.016 0.002 PHE G 20 TYR 0.025 0.002 TYR E 208 ARG 0.008 0.001 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.05155 ( 1137) hydrogen bonds : angle 3.74231 ( 3366) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.52757 ( 8) covalent geometry : bond 0.00449 (15739) covalent geometry : angle 0.52460 (21107) *********************** 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: 19 poor density : 150 time to evaluate : 1.677 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8633 (mtt90) cc_final: 0.8332 (mtm110) REVERT: A 69 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: A 103 LYS cc_start: 0.7649 (ptmm) cc_final: 0.7057 (ttpp) REVERT: B 175 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7615 (tpp-160) REVERT: D 79 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: D 130 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: D 175 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7852 (tpt170) REVERT: E 15 GLU cc_start: 0.8236 (mp0) cc_final: 0.7893 (mp0) REVERT: E 81 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8093 (ttpt) REVERT: E 182 LEU cc_start: 0.8652 (tp) cc_final: 0.8260 (mm) REVERT: E 257 MET cc_start: 0.5034 (mtm) cc_final: 0.4691 (pmm) REVERT: F 98 ARG cc_start: 0.3874 (mtt-85) cc_final: 0.2722 (tpp80) REVERT: F 164 MET cc_start: 0.0413 (OUTLIER) cc_final: 0.0156 (ttt) REVERT: F 214 MET cc_start: 0.5222 (OUTLIER) cc_final: 0.4521 (tpt) REVERT: G 12 ARG cc_start: 0.3461 (tpp-160) cc_final: 0.2084 (mtm180) REVERT: G 15 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5213 (tm-30) REVERT: G 155 LEU cc_start: 0.3176 (tp) cc_final: 0.2230 (mp) REVERT: G 214 MET cc_start: 0.3799 (ptt) cc_final: 0.3455 (ptm) outliers start: 19 outliers final: 7 residues processed: 161 average time/residue: 1.3901 time to fit residues: 246.8009 Evaluate side-chains 161 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 175 ARG 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 76 GLN 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 108 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 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 A 121 GLN B 76 GLN B 121 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.198249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120430 restraints weight = 27309.212| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.99 r_work: 0.3282 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1610 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= 0.128 Angle : 0.471 14.604 21115 Z= 0.245 Chirality : 0.038 0.183 2331 Planarity : 0.004 0.049 2586 Dihedral : 16.553 155.555 2676 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.11 % Allowed : 10.57 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.19), residues: 1827 helix: 3.52 (0.13), residues: 1260 sheet: -0.53 (0.75), residues: 51 loop : -0.38 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 84 HIS 0.002 0.000 HIS D 82 PHE 0.013 0.001 PHE A 212 TYR 0.020 0.001 TYR E 208 ARG 0.006 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 1137) hydrogen bonds : angle 3.61912 ( 3366) SS BOND : bond 0.00101 ( 4) SS BOND : angle 0.44070 ( 8) covalent geometry : bond 0.00288 (15739) covalent geometry : angle 0.47115 (21107) *********************** 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 163 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8635 (mtt90) cc_final: 0.8336 (mtm110) REVERT: A 69 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 103 LYS cc_start: 0.7624 (ptmm) cc_final: 0.7034 (ttpp) REVERT: B 175 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7425 (tpp-160) REVERT: D 130 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: D 159 ASP cc_start: 0.8333 (t0) cc_final: 0.8090 (t70) REVERT: D 175 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7795 (tpt170) REVERT: E 15 GLU cc_start: 0.8275 (mp0) cc_final: 0.7936 (mp0) REVERT: E 81 LYS cc_start: 0.8308 (ttpp) cc_final: 0.8028 (ttpt) REVERT: E 182 LEU cc_start: 0.8652 (tp) cc_final: 0.8231 (mm) REVERT: F 98 ARG cc_start: 0.3911 (mtt-85) cc_final: 0.2680 (tpp80) REVERT: F 164 MET cc_start: 0.0513 (OUTLIER) cc_final: 0.0243 (ttt) REVERT: F 214 MET cc_start: 0.5230 (OUTLIER) cc_final: 0.4399 (tpt) REVERT: G 12 ARG cc_start: 0.3225 (tpp-160) cc_final: 0.2398 (mtm110) REVERT: G 15 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5238 (tm-30) REVERT: G 70 ARG cc_start: 0.2418 (ttp-110) cc_final: 0.1708 (tmm-80) REVERT: G 155 LEU cc_start: 0.3369 (tp) cc_final: 0.2419 (mp) REVERT: G 214 MET cc_start: 0.3801 (ptt) cc_final: 0.3464 (ptm) outliers start: 18 outliers final: 7 residues processed: 156 average time/residue: 1.3627 time to fit residues: 235.7744 Evaluate side-chains 156 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU 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 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 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 158 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.197886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119497 restraints weight = 33230.709| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.71 r_work: 0.3245 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 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 = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15743 Z= 0.137 Angle : 0.478 12.973 21115 Z= 0.249 Chirality : 0.038 0.189 2331 Planarity : 0.004 0.041 2586 Dihedral : 16.306 158.034 2676 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.35 % Allowed : 10.63 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.19), residues: 1827 helix: 3.52 (0.13), residues: 1260 sheet: -0.51 (0.75), residues: 51 loop : -0.37 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 84 HIS 0.003 0.000 HIS D 82 PHE 0.013 0.001 PHE G 20 TYR 0.021 0.001 TYR E 208 ARG 0.005 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 1137) hydrogen bonds : angle 3.61080 ( 3366) SS BOND : bond 0.00073 ( 4) SS BOND : angle 0.40216 ( 8) covalent geometry : bond 0.00314 (15739) covalent geometry : angle 0.47781 (21107) *********************** 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 166 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8460 (mtt90) cc_final: 0.8194 (mtm110) REVERT: A 69 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 103 LYS cc_start: 0.7561 (ptmm) cc_final: 0.6974 (ttpp) REVERT: B 175 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7354 (tpp-160) REVERT: D 130 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: D 175 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7695 (tpt170) REVERT: E 15 GLU cc_start: 0.8157 (mp0) cc_final: 0.7826 (mp0) REVERT: E 81 LYS cc_start: 0.8281 (ttpp) cc_final: 0.8010 (ttpt) REVERT: E 257 MET cc_start: 0.4879 (mtm) cc_final: 0.4592 (pmm) REVERT: F 98 ARG cc_start: 0.3993 (mtt-85) cc_final: 0.2690 (tpp80) REVERT: F 164 MET cc_start: 0.0516 (OUTLIER) cc_final: 0.0193 (ttt) REVERT: F 214 MET cc_start: 0.5024 (OUTLIER) cc_final: 0.4262 (tpt) REVERT: G 12 ARG cc_start: 0.3431 (tpp-160) cc_final: 0.2520 (mtm110) REVERT: G 15 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5170 (tm-30) REVERT: G 155 LEU cc_start: 0.3408 (tp) cc_final: 0.2402 (mp) REVERT: G 214 MET cc_start: 0.3952 (ptt) cc_final: 0.3603 (ptm) outliers start: 22 outliers final: 9 residues processed: 157 average time/residue: 1.5017 time to fit residues: 259.8453 Evaluate side-chains 158 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU 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 69 GLU 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 76 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.197925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120753 restraints weight = 28472.376| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.53 r_work: 0.3260 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15743 Z= 0.139 Angle : 0.480 12.163 21115 Z= 0.250 Chirality : 0.038 0.302 2331 Planarity : 0.004 0.041 2586 Dihedral : 16.224 159.161 2676 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.98 % Allowed : 11.19 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.19), residues: 1827 helix: 3.52 (0.13), residues: 1260 sheet: -0.61 (0.74), residues: 51 loop : -0.37 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 84 HIS 0.003 0.000 HIS D 82 PHE 0.013 0.001 PHE G 20 TYR 0.021 0.001 TYR E 208 ARG 0.005 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 1137) hydrogen bonds : angle 3.60369 ( 3366) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.41358 ( 8) covalent geometry : bond 0.00320 (15739) covalent geometry : angle 0.47967 (21107) *********************** 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 161 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8651 (mtt90) cc_final: 0.8372 (mtm110) REVERT: A 69 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: A 103 LYS cc_start: 0.7652 (ptmm) cc_final: 0.7054 (ttpp) REVERT: B 175 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7586 (tpp-160) REVERT: D 130 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: D 175 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7840 (tpt170) REVERT: E 15 GLU cc_start: 0.8305 (mp0) cc_final: 0.7972 (mp0) REVERT: E 81 LYS cc_start: 0.8341 (ttpp) cc_final: 0.8079 (ttpt) REVERT: E 182 LEU cc_start: 0.8635 (tp) cc_final: 0.8239 (mm) REVERT: E 257 MET cc_start: 0.4979 (mtm) cc_final: 0.4690 (pmm) REVERT: F 98 ARG cc_start: 0.3985 (mtt-85) cc_final: 0.2677 (tpp80) REVERT: F 164 MET cc_start: 0.0571 (OUTLIER) cc_final: 0.0275 (ttt) REVERT: F 214 MET cc_start: 0.5199 (mpp) cc_final: 0.4415 (mmm) REVERT: G 12 ARG cc_start: 0.3364 (tpp-160) cc_final: 0.2391 (mtm110) REVERT: G 15 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5211 (tm-30) REVERT: G 155 LEU cc_start: 0.3354 (tp) cc_final: 0.2412 (mp) REVERT: G 214 MET cc_start: 0.4108 (ptt) cc_final: 0.3772 (ptm) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 1.3819 time to fit residues: 234.3165 Evaluate side-chains 157 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU 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 69 GLU 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 76 GLN 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 Chi-restraints excluded: chain G residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 102 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 146 optimal weight: 6.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 D 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.198114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117796 restraints weight = 25643.978| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.98 r_work: 0.3233 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 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 = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1709 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= 0.129 Angle : 0.478 11.764 21115 Z= 0.249 Chirality : 0.038 0.274 2331 Planarity : 0.004 0.041 2586 Dihedral : 16.163 159.568 2676 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.17 % Allowed : 11.00 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.19), residues: 1827 helix: 3.54 (0.13), residues: 1260 sheet: -0.66 (0.74), residues: 51 loop : -0.37 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 84 HIS 0.002 0.000 HIS D 82 PHE 0.018 0.001 PHE E 75 TYR 0.020 0.001 TYR E 208 ARG 0.005 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 1137) hydrogen bonds : angle 3.60297 ( 3366) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.38773 ( 8) covalent geometry : bond 0.00291 (15739) covalent geometry : angle 0.47829 (21107) ********************** 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 162 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8332 (mtm110) REVERT: A 69 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 103 LYS cc_start: 0.7628 (ptmm) cc_final: 0.7031 (ttpp) REVERT: B 175 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7478 (tpp-160) REVERT: D 130 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: D 175 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7794 (tpt170) REVERT: E 15 GLU cc_start: 0.8300 (mp0) cc_final: 0.7940 (mp0) REVERT: E 81 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8057 (ttpt) REVERT: E 182 LEU cc_start: 0.8609 (tp) cc_final: 0.8201 (mm) REVERT: E 257 MET cc_start: 0.4974 (mtm) cc_final: 0.4693 (pmm) REVERT: F 98 ARG cc_start: 0.3982 (mtt-85) cc_final: 0.2682 (tpp80) REVERT: F 164 MET cc_start: 0.0596 (OUTLIER) cc_final: 0.0303 (ttt) REVERT: F 212 LEU cc_start: 0.2355 (OUTLIER) cc_final: 0.1514 (mt) REVERT: F 214 MET cc_start: 0.5208 (mpp) cc_final: 0.4417 (mmm) REVERT: G 12 ARG cc_start: 0.3377 (tpp-160) cc_final: 0.2423 (mtm110) REVERT: G 15 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5126 (tm-30) REVERT: G 155 LEU cc_start: 0.3339 (tp) cc_final: 0.2399 (mp) REVERT: G 214 MET cc_start: 0.4077 (ptt) cc_final: 0.3743 (ptm) outliers start: 19 outliers final: 9 residues processed: 155 average time/residue: 1.3916 time to fit residues: 238.0341 Evaluate side-chains 158 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU 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 69 GLU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain D residue 121 GLN 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 212 LEU Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 137 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 124 optimal weight: 0.7980 chunk 40 optimal weight: 0.0770 chunk 157 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 152 optimal weight: 0.0000 chunk 53 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 121 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.199146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121467 restraints weight = 21917.108| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.82 r_work: 0.3295 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 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 = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 15743 Z= 0.112 Angle : 0.454 11.867 21115 Z= 0.237 Chirality : 0.037 0.217 2331 Planarity : 0.003 0.041 2586 Dihedral : 15.738 160.351 2676 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.04 % Allowed : 11.25 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.19), residues: 1827 helix: 3.65 (0.13), residues: 1259 sheet: -0.83 (0.76), residues: 49 loop : -0.31 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 84 HIS 0.002 0.000 HIS A 157 PHE 0.014 0.001 PHE A 212 TYR 0.017 0.001 TYR E 208 ARG 0.005 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 1137) hydrogen bonds : angle 3.50881 ( 3366) SS BOND : bond 0.00071 ( 4) SS BOND : angle 0.31897 ( 8) covalent geometry : bond 0.00242 (15739) covalent geometry : angle 0.45439 (21107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17069.97 seconds wall clock time: 293 minutes 34.10 seconds (17614.10 seconds total)