Starting phenix.real_space_refine on Tue Jan 21 01:37:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyk_18756/01_2025/8qyk_18756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyk_18756/01_2025/8qyk_18756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyk_18756/01_2025/8qyk_18756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyk_18756/01_2025/8qyk_18756.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyk_18756/01_2025/8qyk_18756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyk_18756/01_2025/8qyk_18756.cif" } resolution = 2.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 49 5.16 5 C 9997 2.51 5 N 2417 2.21 5 O 3699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16182 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2129 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Conformer: "B" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} bond proxies already assigned to first conformer: 2158 Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "C" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 255} Chain: "D" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "E" Number of atoms: 2127 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Conformer: "B" Number of residues, atoms: 265, 2120 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} bond proxies already assigned to first conformer: 2160 Chain: "F" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "G" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "D" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 163 Classifications: {'water': 163} Link IDs: {None: 162} Chain: "E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 170 Classifications: {'water': 170} Link IDs: {None: 169} Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 13.60, per 1000 atoms: 0.84 Number of scatterers: 16182 At special positions: 0 Unit cell: (84.032, 82.368, 227.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 49 16.00 P 15 15.00 O 3699 8.00 N 2417 7.00 C 9997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 86 " distance=2.03 Simple disulfide: pdb=" SG CYS F 165 " - pdb=" SG CYS F 240 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 86 " distance=2.03 Simple disulfide: pdb=" SG CYS G 165 " - pdb=" SG CYS G 240 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 2.2 seconds 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3476 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 7 sheets defined 78.3% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 17 through 38 Processing helix chain 'A' and resid 38 through 58 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 134 through 158 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 165 through 218 Processing helix chain 'A' and resid 223 through 265 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 13 through 14 No H-bonds generated for 'chain 'B' and resid 13 through 14' Processing helix chain 'B' and resid 15 through 16 No H-bonds generated for 'chain 'B' and resid 15 through 16' Processing helix chain 'B' and resid 17 through 38 Processing helix chain 'B' and resid 38 through 58 Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 134 through 158 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 165 through 218 Processing helix chain 'B' and resid 223 through 265 removed outlier: 3.566A pdb=" N GLU B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 14 through 16 No H-bonds generated for 'chain 'C' and resid 14 through 16' Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 38 through 59 Processing helix chain 'C' and resid 63 through 75 Processing helix chain 'C' and resid 77 through 90 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 162 through 220 removed outlier: 3.723A pdb=" N LEU C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 265 removed outlier: 3.544A pdb=" N GLU C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 17 through 38 removed outlier: 3.504A pdb=" N VAL D 21 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 58 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.485A pdb=" N ARG D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 134 through 158 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 165 through 220 removed outlier: 3.805A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 265 removed outlier: 3.582A pdb=" N GLU D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 17 through 38 Processing helix chain 'E' and resid 38 through 58 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 77 through 90 Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 134 through 157 Processing helix chain 'E' and resid 162 through 218 Processing helix chain 'E' and resid 223 through 265 Processing helix chain 'F' and resid 19 through 79 Processing helix chain 'F' and resid 107 through 127 removed outlier: 3.736A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 148 through 169 Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.876A pdb=" N LYS F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 203 through 208 removed outlier: 3.514A pdb=" N ARG F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 47 removed outlier: 3.976A pdb=" N ILE G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 79 Processing helix chain 'G' and resid 107 through 127 Proline residue: G 119 - end of helix removed outlier: 3.517A pdb=" N SER G 127 " --> pdb=" O GLU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 133 Processing helix chain 'G' and resid 148 through 168 removed outlier: 3.541A pdb=" N ASN G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 177 removed outlier: 3.618A pdb=" N LYS G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN G 177 " --> pdb=" O PRO G 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 177' Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'G' and resid 203 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 98 removed outlier: 3.631A pdb=" N ARG A 106 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 96 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE A 104 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU A 98 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 98 removed outlier: 3.698A pdb=" N ARG B 106 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU B 96 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE B 104 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU B 98 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 97 removed outlier: 3.689A pdb=" N ARG C 106 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU C 96 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 104 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 98 removed outlier: 3.766A pdb=" N ARG D 106 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU D 96 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE D 104 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU D 98 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 98 removed outlier: 3.690A pdb=" N ARG E 106 " --> pdb=" O GLN E 94 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU E 96 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE E 104 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLU E 98 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 82 through 85 removed outlier: 5.025A pdb=" N PHE F 93 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL F 210 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLU F 211 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE F 139 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG F 213 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE F 137 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLN F 215 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER F 196 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY F 141 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 83 through 85 removed outlier: 3.537A pdb=" N VAL G 83 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU G 211 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN G 215 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN G 136 " --> pdb=" O GLN G 215 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N LEU G 191 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE G 137 " --> pdb=" O LEU G 191 " (cutoff:3.500A) 1126 hydrogen bonds defined for protein. 3327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2406 1.28 - 1.41: 3760 1.41 - 1.54: 9147 1.54 - 1.68: 201 1.68 - 1.81: 95 Bond restraints: 15609 Sorted by residual: bond pdb=" C38 PEE B 502 " pdb=" C39 PEE B 502 " ideal model delta sigma weight residual 1.523 1.353 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C38 PEE E 502 " pdb=" C39 PEE E 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" C38 PEE C 502 " pdb=" C39 PEE C 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C38 PEE A 502 " pdb=" C39 PEE A 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" C38 PEE D 502 " pdb=" C39 PEE D 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.11e+01 ... (remaining 15604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.41: 20903 10.41 - 20.82: 19 20.82 - 31.23: 0 31.23 - 41.65: 0 41.65 - 52.06: 10 Bond angle restraints: 20932 Sorted by residual: angle pdb=" C38 PEE D 502 " pdb=" C39 PEE D 502 " pdb=" C40 PEE D 502 " ideal model delta sigma weight residual 112.47 164.53 -52.06 3.00e+00 1.11e-01 3.01e+02 angle pdb=" C38 PEE A 502 " pdb=" C39 PEE A 502 " pdb=" C40 PEE A 502 " ideal model delta sigma weight residual 112.47 164.23 -51.76 3.00e+00 1.11e-01 2.98e+02 angle pdb=" C38 PEE E 502 " pdb=" C39 PEE E 502 " pdb=" C40 PEE E 502 " ideal model delta sigma weight residual 112.47 164.05 -51.58 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C38 PEE B 502 " pdb=" C39 PEE B 502 " pdb=" C40 PEE B 502 " ideal model delta sigma weight residual 112.47 163.83 -51.36 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C38 PEE C 502 " pdb=" C39 PEE C 502 " pdb=" C40 PEE C 502 " ideal model delta sigma weight residual 112.47 163.55 -51.08 3.00e+00 1.11e-01 2.90e+02 ... (remaining 20927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 9192 32.97 - 65.94: 377 65.94 - 98.90: 37 98.90 - 131.87: 19 131.87 - 164.84: 12 Dihedral angle restraints: 9637 sinusoidal: 4286 harmonic: 5351 Sorted by residual: dihedral pdb=" CD ARG F 52 " pdb=" NE ARG F 52 " pdb=" CZ ARG F 52 " pdb=" NH1 ARG F 52 " ideal model delta sinusoidal sigma weight residual 0.00 -72.81 72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" C3 PEE D 502 " pdb=" C1 PEE D 502 " pdb=" C2 PEE D 502 " pdb=" O3P PEE D 502 " ideal model delta sinusoidal sigma weight residual 62.73 -102.11 164.84 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C3 PEE B 502 " pdb=" C1 PEE B 502 " pdb=" C2 PEE B 502 " pdb=" O3P PEE B 502 " ideal model delta sinusoidal sigma weight residual 62.73 -99.08 161.81 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 9634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2267 0.111 - 0.221: 32 0.221 - 0.332: 1 0.332 - 0.442: 1 0.442 - 0.553: 5 Chirality restraints: 2306 Sorted by residual: chirality pdb=" C2 PEE E 502 " pdb=" C1 PEE E 502 " pdb=" C3 PEE E 502 " pdb=" O2 PEE E 502 " both_signs ideal model delta sigma weight residual False -2.33 -2.88 0.55 2.00e-01 2.50e+01 7.64e+00 chirality pdb=" C2 PEE B 502 " pdb=" C1 PEE B 502 " pdb=" C3 PEE B 502 " pdb=" O2 PEE B 502 " both_signs ideal model delta sigma weight residual False -2.33 -2.88 0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" C2 PEE D 502 " pdb=" C1 PEE D 502 " pdb=" C3 PEE D 502 " pdb=" O2 PEE D 502 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.55 2.00e-01 2.50e+01 7.48e+00 ... (remaining 2303 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 52 " -1.028 9.50e-02 1.11e+02 4.61e-01 1.28e+02 pdb=" NE ARG F 52 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG F 52 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 52 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 52 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 12 " -0.676 9.50e-02 1.11e+02 3.03e-01 5.59e+01 pdb=" NE ARG G 12 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG G 12 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 12 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 12 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 49 " -0.239 9.50e-02 1.11e+02 1.07e-01 7.22e+00 pdb=" NE ARG F 49 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG F 49 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 49 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 49 " -0.006 2.00e-02 2.50e+03 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 565 2.68 - 3.23: 15728 3.23 - 3.79: 28914 3.79 - 4.34: 37400 4.34 - 4.90: 60121 Nonbonded interactions: 142728 Sorted by model distance: nonbonded pdb=" O HOH E 642 " pdb=" O HOH E 669 " model vdw 2.122 3.040 nonbonded pdb=" O HOH D 610 " pdb=" O HOH D 744 " model vdw 2.137 3.040 nonbonded pdb=" O LYS G 18 " pdb=" O HOH G 301 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASN B 5 " pdb=" NH2 ARG C 175 " model vdw 2.159 3.120 nonbonded pdb=" OH TYR E 208 " pdb=" OA4 CDL E 501 " model vdw 2.166 3.040 ... (remaining 142723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 265 or resid 501 through 503)) selection = (chain 'B' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 265 or resid 501 through 503)) selection = (chain 'C' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 265 or resid 501 through 503)) selection = (chain 'D' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 265 or resid 501 through 503)) selection = (chain 'E' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 265 or resid 501 through 503)) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.880 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.450 Find NCS groups from input model: 0.730 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: 0.000 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 15609 Z= 0.538 Angle : 1.373 52.057 20932 Z= 0.530 Chirality : 0.048 0.553 2306 Planarity : 0.012 0.461 2566 Dihedral : 18.956 164.839 6149 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.19 % Allowed : 0.25 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.20), residues: 1807 helix: 3.39 (0.13), residues: 1266 sheet: -0.97 (0.89), residues: 36 loop : -0.27 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 84 HIS 0.005 0.001 HIS D 82 PHE 0.021 0.002 PHE A 181 TYR 0.023 0.002 TYR E 208 ARG 0.008 0.001 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8841 (m-80) cc_final: 0.8598 (m-80) REVERT: B 5 ASN cc_start: 0.7260 (m-40) cc_final: 0.6884 (m110) REVERT: B 69 GLU cc_start: 0.7503 (pp20) cc_final: 0.7273 (pp20) REVERT: B 102 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6310 (mm-30) REVERT: B 152 MET cc_start: 0.9125 (mtm) cc_final: 0.8872 (mtp) REVERT: C 11 LEU cc_start: 0.8503 (mt) cc_final: 0.8289 (mt) REVERT: F 244 MET cc_start: 0.1672 (ptp) cc_final: 0.1452 (pmm) REVERT: G 11 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.5495 (ptp-170) REVERT: G 164 MET cc_start: 0.3067 (ttm) cc_final: 0.2373 (ttt) REVERT: G 244 MET cc_start: 0.0484 (mtt) cc_final: 0.0216 (tpp) outliers start: 3 outliers final: 0 residues processed: 181 average time/residue: 1.7793 time to fit residues: 348.5030 Evaluate side-chains 146 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 161 optimal weight: 0.2980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 134 HIS B 157 HIS C 121 GLN D 165 GLN E 134 HIS E 171 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.207539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120685 restraints weight = 21016.351| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.03 r_work: 0.3233 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15609 Z= 0.246 Angle : 0.564 8.136 20932 Z= 0.293 Chirality : 0.041 0.168 2306 Planarity : 0.004 0.056 2566 Dihedral : 19.172 177.099 2659 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.74 % Allowed : 4.82 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.20), residues: 1807 helix: 3.34 (0.13), residues: 1272 sheet: -1.40 (0.82), residues: 36 loop : -0.30 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 84 HIS 0.006 0.001 HIS B 82 PHE 0.022 0.002 PHE A 181 TYR 0.024 0.002 TYR B 208 ARG 0.005 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3412 (mtp) cc_final: 0.3145 (ttt) REVERT: B 44 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8037 (ttp-170) REVERT: B 61 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8551 (mtpt) REVERT: B 102 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6857 (mm-30) REVERT: B 152 MET cc_start: 0.9106 (mtm) cc_final: 0.8838 (mtp) REVERT: C 11 LEU cc_start: 0.8611 (mt) cc_final: 0.8370 (mt) REVERT: C 61 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8160 (mptt) REVERT: D 130 GLU cc_start: 0.8199 (mp0) cc_final: 0.7311 (pm20) REVERT: E 65 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: F 122 LEU cc_start: 0.2336 (mm) cc_final: 0.2120 (pp) REVERT: F 244 MET cc_start: 0.1451 (ptp) cc_final: 0.1241 (pmm) REVERT: G 11 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5521 (ptp-170) REVERT: G 164 MET cc_start: 0.2843 (ttm) cc_final: 0.2347 (ttp) REVERT: G 244 MET cc_start: 0.0405 (mtt) cc_final: 0.0171 (tpp) outliers start: 12 outliers final: 5 residues processed: 164 average time/residue: 1.7732 time to fit residues: 316.4555 Evaluate side-chains 153 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain G residue 11 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 121 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN C 121 GLN E 171 ASN F 87 HIS F 241 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.208823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123052 restraints weight = 23341.526| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.30 r_work: 0.3258 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15609 Z= 0.177 Angle : 0.494 8.690 20932 Z= 0.258 Chirality : 0.038 0.173 2306 Planarity : 0.004 0.053 2566 Dihedral : 18.118 178.514 2659 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.80 % Allowed : 6.43 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.20), residues: 1807 helix: 3.53 (0.13), residues: 1264 sheet: -1.09 (0.74), residues: 46 loop : -0.06 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 84 HIS 0.005 0.001 HIS B 82 PHE 0.016 0.001 PHE A 181 TYR 0.019 0.001 TYR B 208 ARG 0.003 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3218 (mtp) cc_final: 0.2982 (ttt) REVERT: B 69 GLU cc_start: 0.7474 (pp20) cc_final: 0.7257 (pp20) REVERT: B 102 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7016 (mm-30) REVERT: B 152 MET cc_start: 0.9055 (mtm) cc_final: 0.8803 (mtp) REVERT: C 11 LEU cc_start: 0.8578 (mt) cc_final: 0.8351 (mt) REVERT: C 61 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8036 (mptt) REVERT: D 130 GLU cc_start: 0.8145 (mp0) cc_final: 0.7275 (pm20) REVERT: D 257 MET cc_start: 0.3184 (OUTLIER) cc_final: 0.1932 (mtp) REVERT: E 65 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: E 72 LYS cc_start: 0.8388 (tptt) cc_final: 0.8081 (tttp) REVERT: F 1 MET cc_start: 0.5176 (OUTLIER) cc_final: 0.4624 (ttt) REVERT: F 4 ASN cc_start: 0.6243 (p0) cc_final: 0.5889 (t0) REVERT: F 244 MET cc_start: 0.1508 (ptp) cc_final: 0.1305 (pmm) REVERT: G 11 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5806 (ptt-90) REVERT: G 51 GLN cc_start: 0.6945 (mt0) cc_final: 0.6390 (mt0) REVERT: G 164 MET cc_start: 0.2520 (ttm) cc_final: 0.2035 (ttp) REVERT: G 244 MET cc_start: 0.0410 (mtt) cc_final: 0.0187 (tpp) outliers start: 13 outliers final: 3 residues processed: 165 average time/residue: 1.6463 time to fit residues: 296.4223 Evaluate side-chains 154 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 11 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 130 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 152 optimal weight: 0.0470 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN E 171 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123090 restraints weight = 24286.706| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.36 r_work: 0.3206 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 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 = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15609 Z= 0.212 Angle : 0.520 8.339 20932 Z= 0.272 Chirality : 0.039 0.158 2306 Planarity : 0.004 0.058 2566 Dihedral : 17.692 178.588 2659 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.05 % Allowed : 7.48 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.19), residues: 1807 helix: 3.43 (0.13), residues: 1269 sheet: -1.13 (0.73), residues: 46 loop : -0.08 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 84 HIS 0.005 0.001 HIS D 82 PHE 0.020 0.002 PHE A 181 TYR 0.023 0.002 TYR B 208 ARG 0.003 0.000 ARG G 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3300 (mtp) cc_final: 0.2887 (ttt) REVERT: B 44 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8578 (mtp180) REVERT: B 61 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8657 (mtpt) REVERT: B 69 GLU cc_start: 0.7574 (pp20) cc_final: 0.7329 (pp20) REVERT: B 102 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7152 (mm-30) REVERT: B 152 MET cc_start: 0.9088 (mtm) cc_final: 0.8827 (mtp) REVERT: C 61 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8128 (mptt) REVERT: D 130 GLU cc_start: 0.8264 (mp0) cc_final: 0.7375 (pm20) REVERT: E 65 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: E 72 LYS cc_start: 0.8422 (tptt) cc_final: 0.8113 (tttp) REVERT: F 1 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.4787 (ttt) REVERT: F 4 ASN cc_start: 0.6245 (p0) cc_final: 0.5886 (t0) REVERT: F 51 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: F 212 LEU cc_start: 0.1451 (tp) cc_final: 0.1240 (tm) REVERT: G 15 GLU cc_start: 0.5934 (tp30) cc_final: 0.5719 (tp30) REVERT: G 164 MET cc_start: 0.2289 (ttm) cc_final: 0.1837 (ttp) REVERT: G 244 MET cc_start: 0.0384 (mtt) cc_final: 0.0102 (tpp) outliers start: 17 outliers final: 4 residues processed: 172 average time/residue: 1.7083 time to fit residues: 319.7315 Evaluate side-chains 159 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 51 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 83 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN D 121 GLN E 171 ASN G 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.207333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122628 restraints weight = 23632.018| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.34 r_work: 0.3215 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 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 = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15609 Z= 0.206 Angle : 0.516 8.808 20932 Z= 0.270 Chirality : 0.039 0.230 2306 Planarity : 0.004 0.057 2566 Dihedral : 17.352 178.201 2655 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.93 % Allowed : 8.35 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.19), residues: 1807 helix: 3.49 (0.13), residues: 1263 sheet: -1.10 (0.72), residues: 46 loop : -0.00 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 84 HIS 0.005 0.001 HIS D 82 PHE 0.019 0.002 PHE A 181 TYR 0.024 0.002 TYR B 208 ARG 0.003 0.000 ARG G 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8322 (mt) cc_final: 0.7990 (mp) REVERT: B 44 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8139 (ttp-170) REVERT: B 61 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8634 (mtpt) REVERT: B 69 GLU cc_start: 0.7612 (pp20) cc_final: 0.7346 (pp20) REVERT: B 102 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7201 (mm-30) REVERT: B 152 MET cc_start: 0.9058 (mtm) cc_final: 0.8794 (mtp) REVERT: C 61 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8112 (mptt) REVERT: D 11 LEU cc_start: 0.7669 (mt) cc_final: 0.7367 (mp) REVERT: D 130 GLU cc_start: 0.8270 (mp0) cc_final: 0.7382 (pm20) REVERT: E 65 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: E 72 LYS cc_start: 0.8424 (tptt) cc_final: 0.8111 (tttp) REVERT: F 1 MET cc_start: 0.5445 (OUTLIER) cc_final: 0.4668 (ttt) REVERT: F 51 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: F 122 LEU cc_start: 0.2434 (mm) cc_final: 0.2169 (pp) REVERT: G 164 MET cc_start: 0.2498 (ttm) cc_final: 0.2089 (ttp) REVERT: G 214 MET cc_start: 0.1511 (pmm) cc_final: 0.1019 (ttp) REVERT: G 244 MET cc_start: 0.0356 (mtt) cc_final: -0.0338 (tpp) outliers start: 15 outliers final: 4 residues processed: 160 average time/residue: 1.5707 time to fit residues: 275.2559 Evaluate side-chains 156 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 51 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN D 121 GLN E 171 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.207442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122803 restraints weight = 21037.681| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.56 r_work: 0.3235 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15609 Z= 0.201 Angle : 0.516 11.572 20932 Z= 0.269 Chirality : 0.039 0.244 2306 Planarity : 0.004 0.057 2566 Dihedral : 17.113 179.308 2655 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.11 % Allowed : 8.53 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.19), residues: 1807 helix: 3.47 (0.13), residues: 1269 sheet: -0.96 (0.73), residues: 46 loop : -0.08 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 84 HIS 0.005 0.001 HIS D 82 PHE 0.019 0.002 PHE A 181 TYR 0.024 0.002 TYR B 208 ARG 0.004 0.000 ARG G 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8010 (ttp-170) REVERT: B 61 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8623 (mtpt) REVERT: B 69 GLU cc_start: 0.7563 (pp20) cc_final: 0.7300 (pp20) REVERT: B 102 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 152 MET cc_start: 0.8999 (mtm) cc_final: 0.8744 (mtp) REVERT: C 61 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8103 (mptt) REVERT: D 11 LEU cc_start: 0.7625 (mt) cc_final: 0.7342 (mp) REVERT: D 130 GLU cc_start: 0.8109 (mp0) cc_final: 0.7223 (pm20) REVERT: E 65 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: E 72 LYS cc_start: 0.8372 (tptt) cc_final: 0.8060 (tttp) REVERT: F 1 MET cc_start: 0.5238 (OUTLIER) cc_final: 0.4255 (ttt) REVERT: F 55 GLN cc_start: 0.6073 (mm-40) cc_final: 0.5868 (mm-40) REVERT: G 164 MET cc_start: 0.2410 (ttm) cc_final: 0.2024 (ttp) REVERT: G 244 MET cc_start: 0.0120 (mtt) cc_final: -0.0468 (tpp) outliers start: 18 outliers final: 5 residues processed: 161 average time/residue: 1.5664 time to fit residues: 275.9165 Evaluate side-chains 159 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 51 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN E 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.208544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122202 restraints weight = 24180.747| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.68 r_work: 0.3236 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15609 Z= 0.185 Angle : 0.504 8.672 20932 Z= 0.262 Chirality : 0.039 0.278 2306 Planarity : 0.004 0.055 2566 Dihedral : 16.851 178.452 2655 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.30 % Allowed : 8.78 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.19), residues: 1807 helix: 3.56 (0.13), residues: 1264 sheet: -0.97 (0.71), residues: 46 loop : -0.03 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 84 HIS 0.005 0.001 HIS D 82 PHE 0.017 0.001 PHE A 181 TYR 0.022 0.002 TYR B 208 ARG 0.003 0.000 ARG G 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8045 (ttp-170) REVERT: B 61 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8598 (mtpt) REVERT: B 69 GLU cc_start: 0.7533 (pp20) cc_final: 0.7274 (pp20) REVERT: B 102 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 152 MET cc_start: 0.8996 (mtm) cc_final: 0.8742 (mtp) REVERT: C 61 LYS cc_start: 0.8428 (mmtm) cc_final: 0.8114 (mptt) REVERT: D 11 LEU cc_start: 0.7588 (mt) cc_final: 0.7327 (mp) REVERT: D 130 GLU cc_start: 0.8136 (mp0) cc_final: 0.7256 (pm20) REVERT: E 65 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: E 72 LYS cc_start: 0.8368 (tptt) cc_final: 0.8057 (tttp) REVERT: F 1 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.4411 (ttt) REVERT: G 164 MET cc_start: 0.2467 (ttm) cc_final: 0.2086 (ttp) REVERT: G 214 MET cc_start: 0.1375 (pmm) cc_final: 0.0974 (ttp) REVERT: G 244 MET cc_start: 0.0161 (mtt) cc_final: -0.0465 (tpp) outliers start: 21 outliers final: 5 residues processed: 169 average time/residue: 1.5551 time to fit residues: 287.8740 Evaluate side-chains 160 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 51 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 121 GLN E 171 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.207407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123831 restraints weight = 15609.009| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.39 r_work: 0.3258 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15609 Z= 0.219 Angle : 0.536 9.368 20932 Z= 0.279 Chirality : 0.039 0.228 2306 Planarity : 0.004 0.054 2566 Dihedral : 16.990 178.948 2655 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.99 % Allowed : 9.40 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.19), residues: 1807 helix: 3.44 (0.13), residues: 1269 sheet: -1.10 (0.70), residues: 46 loop : -0.10 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 84 HIS 0.006 0.001 HIS D 82 PHE 0.020 0.002 PHE A 181 TYR 0.027 0.002 TYR B 208 ARG 0.003 0.000 ARG G 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7955 (ttp-170) REVERT: B 61 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8624 (mtpt) REVERT: B 69 GLU cc_start: 0.7539 (pp20) cc_final: 0.7304 (pp20) REVERT: B 102 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7291 (mm-30) REVERT: B 152 MET cc_start: 0.8984 (mtm) cc_final: 0.8723 (mtp) REVERT: C 61 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8120 (mptt) REVERT: D 11 LEU cc_start: 0.7671 (mt) cc_final: 0.7410 (mp) REVERT: D 130 GLU cc_start: 0.8089 (mp0) cc_final: 0.7205 (pm20) REVERT: E 65 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: E 72 LYS cc_start: 0.8352 (tptt) cc_final: 0.8049 (tttp) REVERT: F 1 MET cc_start: 0.5251 (OUTLIER) cc_final: 0.4375 (ttt) REVERT: G 51 GLN cc_start: 0.6667 (mt0) cc_final: 0.5952 (mt0) REVERT: G 214 MET cc_start: 0.1433 (pmm) cc_final: 0.0946 (ttp) REVERT: G 244 MET cc_start: 0.0266 (mtt) cc_final: -0.0406 (tpp) outliers start: 16 outliers final: 9 residues processed: 156 average time/residue: 1.6202 time to fit residues: 276.8109 Evaluate side-chains 157 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 177 optimal weight: 20.0000 chunk 7 optimal weight: 0.3980 chunk 168 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 100 optimal weight: 0.6980 chunk 152 optimal weight: 0.0570 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN E 171 ASN F 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.210499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126520 restraints weight = 19980.595| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.55 r_work: 0.3294 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 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 = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15609 Z= 0.151 Angle : 0.481 9.426 20932 Z= 0.250 Chirality : 0.037 0.226 2306 Planarity : 0.004 0.056 2566 Dihedral : 16.459 179.465 2655 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.74 % Allowed : 10.02 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.20), residues: 1807 helix: 3.70 (0.13), residues: 1263 sheet: -0.87 (0.74), residues: 47 loop : -0.01 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 84 HIS 0.004 0.001 HIS A 134 PHE 0.014 0.001 PHE D 212 TYR 0.022 0.001 TYR A 17 ARG 0.002 0.000 ARG G 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8224 (mt) cc_final: 0.7878 (mp) REVERT: B 44 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8024 (ttp-170) REVERT: B 102 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7243 (mm-30) REVERT: B 152 MET cc_start: 0.8917 (mtm) cc_final: 0.8693 (mtp) REVERT: C 61 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8015 (mptt) REVERT: D 11 LEU cc_start: 0.7511 (mt) cc_final: 0.7283 (mp) REVERT: D 130 GLU cc_start: 0.8007 (mp0) cc_final: 0.7175 (pm20) REVERT: E 65 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: E 72 LYS cc_start: 0.8304 (tptt) cc_final: 0.7998 (tttp) REVERT: F 1 MET cc_start: 0.5210 (OUTLIER) cc_final: 0.4352 (ttt) REVERT: F 4 ASN cc_start: 0.6353 (p0) cc_final: 0.6051 (t0) REVERT: F 153 LEU cc_start: 0.2315 (tp) cc_final: 0.1920 (mm) REVERT: G 106 LEU cc_start: -0.0101 (mt) cc_final: -0.0685 (tp) REVERT: G 214 MET cc_start: 0.1467 (pmm) cc_final: 0.0984 (ttp) REVERT: G 244 MET cc_start: 0.0225 (mtt) cc_final: -0.0408 (tpp) outliers start: 12 outliers final: 4 residues processed: 159 average time/residue: 1.4944 time to fit residues: 261.0007 Evaluate side-chains 155 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 29 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 153 optimal weight: 0.0050 chunk 38 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 151 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.209687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124148 restraints weight = 22199.534| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.14 r_work: 0.3250 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15609 Z= 0.168 Angle : 0.499 9.816 20932 Z= 0.257 Chirality : 0.037 0.259 2306 Planarity : 0.004 0.055 2566 Dihedral : 16.309 178.990 2655 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.56 % Allowed : 10.39 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.20), residues: 1807 helix: 3.68 (0.13), residues: 1263 sheet: -0.77 (0.66), residues: 57 loop : -0.03 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 84 HIS 0.005 0.001 HIS D 82 PHE 0.015 0.001 PHE A 181 TYR 0.021 0.001 TYR A 17 ARG 0.003 0.000 ARG G 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8249 (mt) cc_final: 0.7908 (mp) REVERT: B 44 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8060 (ttp-170) REVERT: B 152 MET cc_start: 0.8964 (mtm) cc_final: 0.8716 (mtp) REVERT: C 61 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8064 (mptt) REVERT: D 11 LEU cc_start: 0.7521 (mt) cc_final: 0.7275 (mp) REVERT: D 130 GLU cc_start: 0.8087 (mp0) cc_final: 0.7215 (pm20) REVERT: E 65 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: E 72 LYS cc_start: 0.8339 (tptt) cc_final: 0.8016 (tttp) REVERT: F 1 MET cc_start: 0.5287 (OUTLIER) cc_final: 0.4412 (ttt) REVERT: F 4 ASN cc_start: 0.6176 (p0) cc_final: 0.5826 (t0) REVERT: F 153 LEU cc_start: 0.2380 (tp) cc_final: 0.2006 (mm) REVERT: G 4 ASN cc_start: 0.6902 (OUTLIER) cc_final: 0.6630 (t0) REVERT: G 106 LEU cc_start: -0.0054 (mt) cc_final: -0.0635 (tp) REVERT: G 214 MET cc_start: 0.1555 (pmm) cc_final: 0.1119 (ttp) REVERT: G 244 MET cc_start: 0.0158 (mtt) cc_final: -0.0424 (tpp) outliers start: 9 outliers final: 4 residues processed: 159 average time/residue: 1.6369 time to fit residues: 283.7999 Evaluate side-chains 160 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 157 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 176 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 165 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.208360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123252 restraints weight = 20687.487| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.57 r_work: 0.3246 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15609 Z= 0.189 Angle : 0.518 9.838 20932 Z= 0.268 Chirality : 0.038 0.245 2306 Planarity : 0.004 0.055 2566 Dihedral : 16.340 178.154 2655 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.68 % Allowed : 10.20 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.20), residues: 1807 helix: 3.54 (0.13), residues: 1273 sheet: -1.05 (0.70), residues: 47 loop : -0.23 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 84 HIS 0.005 0.001 HIS D 82 PHE 0.018 0.002 PHE A 181 TYR 0.022 0.002 TYR B 208 ARG 0.003 0.000 ARG G 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20792.19 seconds wall clock time: 368 minutes 10.46 seconds (22090.46 seconds total)