Starting phenix.real_space_refine on Tue Dec 31 15:53:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyk_18756/12_2024/8qyk_18756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyk_18756/12_2024/8qyk_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_18756/12_2024/8qyk_18756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyk_18756/12_2024/8qyk_18756.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyk_18756/12_2024/8qyk_18756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyk_18756/12_2024/8qyk_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 13.54, 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: 4.39 Conformation dependent library (CDL) restraints added in 2.8 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: 1.44 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: 5.35 Time building geometry restraints manager: 5.01 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: 13.430 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: 0.000 Extract box with map and model: 2.340 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.170 Find NCS groups from input model: 0.760 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:15.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.480 ------------------------------------------------------------------------------- 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 : 1.691 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: 1.7615 time to fit residues: 346.6813 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 : 1.875 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3523 (mtp) cc_final: 0.3253 (ttt) REVERT: B 44 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7744 (ttp-170) REVERT: B 61 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8401 (mtpt) REVERT: B 102 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6546 (mm-30) REVERT: B 152 MET cc_start: 0.9133 (mtm) cc_final: 0.8870 (mtp) REVERT: C 11 LEU cc_start: 0.8614 (mt) cc_final: 0.8380 (mt) REVERT: D 130 GLU cc_start: 0.8156 (mp0) cc_final: 0.7333 (pm20) REVERT: E 65 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: F 122 LEU cc_start: 0.2482 (mm) cc_final: 0.2191 (pp) REVERT: F 244 MET cc_start: 0.1447 (ptp) cc_final: 0.1241 (pmm) REVERT: G 11 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.5680 (ptp-170) REVERT: G 164 MET cc_start: 0.2797 (ttm) cc_final: 0.2224 (ttp) REVERT: G 244 MET cc_start: 0.0489 (mtt) cc_final: 0.0212 (tpp) outliers start: 12 outliers final: 5 residues processed: 164 average time/residue: 1.8786 time to fit residues: 338.2389 Evaluate side-chains 152 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 89 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 157 HIS C 121 GLN C 165 GLN E 171 ASN F 241 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 15609 Z= 0.477 Angle : 0.741 8.567 20932 Z= 0.386 Chirality : 0.052 0.210 2306 Planarity : 0.006 0.079 2566 Dihedral : 19.691 176.166 2659 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.11 % Allowed : 7.24 % Favored : 91.65 % 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: 2.70 (0.19), residues: 1807 helix: 2.69 (0.13), residues: 1270 sheet: -1.49 (0.78), residues: 36 loop : -0.37 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 84 HIS 0.010 0.002 HIS D 82 PHE 0.037 0.003 PHE A 181 TYR 0.036 0.003 TYR B 208 ARG 0.009 0.001 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 171 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7647 (mp0) cc_final: 0.7361 (mm-30) REVERT: A 60 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: B 44 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8348 (mtp180) REVERT: B 61 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8483 (mtpt) REVERT: B 102 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6852 (mm-30) REVERT: B 167 SER cc_start: 0.8675 (m) cc_final: 0.8434 (t) REVERT: C 77 ARG cc_start: 0.7201 (ttp-110) cc_final: 0.6998 (ttp-110) REVERT: C 165 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7866 (mm-40) REVERT: D 11 LEU cc_start: 0.7887 (mt) cc_final: 0.7521 (mp) REVERT: E 65 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: F 212 LEU cc_start: 0.1744 (tp) cc_final: 0.1517 (tm) REVERT: G 11 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6179 (ptp90) REVERT: G 164 MET cc_start: 0.2583 (ttm) cc_final: 0.1986 (ttp) REVERT: G 191 LEU cc_start: 0.2078 (pt) cc_final: 0.1845 (pp) REVERT: G 214 MET cc_start: 0.1636 (pmm) cc_final: 0.1108 (ttp) REVERT: G 244 MET cc_start: 0.0379 (mtt) cc_final: -0.0299 (tpp) outliers start: 18 outliers final: 6 residues processed: 164 average time/residue: 1.6954 time to fit residues: 303.0270 Evaluate side-chains 154 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 52 ARG 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 159 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 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 76 GLN C 121 GLN E 171 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15609 Z= 0.193 Angle : 0.517 8.279 20932 Z= 0.270 Chirality : 0.039 0.217 2306 Planarity : 0.004 0.059 2566 Dihedral : 18.277 176.445 2659 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.42 % Allowed : 8.16 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.42 (0.19), residues: 1807 helix: 3.26 (0.13), residues: 1276 sheet: -1.49 (0.78), residues: 36 loop : -0.24 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 84 HIS 0.005 0.001 HIS D 82 PHE 0.015 0.001 PHE D 131 TYR 0.018 0.001 TYR B 208 ARG 0.008 0.000 ARG A 77 *********************** 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: 23 poor density : 158 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7626 (mp0) cc_final: 0.7355 (mm-30) REVERT: B 61 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8455 (mtpt) REVERT: B 102 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7015 (mm-30) REVERT: C 165 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7941 (mm-40) REVERT: D 11 LEU cc_start: 0.7717 (mt) cc_final: 0.7439 (mp) REVERT: E 65 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: F 1 MET cc_start: 0.4951 (OUTLIER) cc_final: 0.4003 (ttt) REVERT: F 122 LEU cc_start: 0.2394 (mm) cc_final: 0.2109 (pp) REVERT: F 212 LEU cc_start: 0.1673 (tp) cc_final: 0.1435 (tm) REVERT: G 164 MET cc_start: 0.2215 (ttm) cc_final: 0.1701 (ttp) REVERT: G 244 MET cc_start: 0.0386 (mtt) cc_final: -0.0300 (tpp) outliers start: 23 outliers final: 5 residues processed: 168 average time/residue: 1.6526 time to fit residues: 306.1938 Evaluate side-chains 159 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain 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 51 GLN Chi-restraints excluded: chain F residue 214 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 121 GLN B 165 GLN C 76 GLN C 121 GLN E 171 ASN F 87 HIS G 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1823 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= 0.193 Angle : 0.515 8.788 20932 Z= 0.269 Chirality : 0.039 0.222 2306 Planarity : 0.004 0.058 2566 Dihedral : 17.566 178.832 2655 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.24 % Allowed : 9.09 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.50 (0.19), residues: 1807 helix: 3.35 (0.13), residues: 1276 sheet: -1.56 (0.67), residues: 46 loop : -0.25 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 84 HIS 0.005 0.001 HIS D 82 PHE 0.018 0.002 PHE A 181 TYR 0.023 0.002 TYR B 208 ARG 0.007 0.000 ARG A 77 *********************** 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 175 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8453 (mtpt) REVERT: D 11 LEU cc_start: 0.7537 (mt) cc_final: 0.7259 (mp) REVERT: E 65 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: F 1 MET cc_start: 0.4738 (OUTLIER) cc_final: 0.3727 (ttt) REVERT: F 122 LEU cc_start: 0.2523 (mm) cc_final: 0.2231 (pp) REVERT: F 212 LEU cc_start: 0.1723 (tp) cc_final: 0.1496 (tm) REVERT: G 164 MET cc_start: 0.2149 (ttm) cc_final: 0.1647 (ttp) REVERT: G 214 MET cc_start: 0.1450 (pmm) cc_final: 0.0948 (ttp) REVERT: G 244 MET cc_start: 0.0420 (mtt) cc_final: 0.0025 (tpp) outliers start: 20 outliers final: 6 residues processed: 165 average time/residue: 1.6701 time to fit residues: 303.1676 Evaluate side-chains 154 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 2.024 ------------------------------------------------------------------------------- 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 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 51 GLN Chi-restraints excluded: chain F residue 214 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15609 Z= 0.317 Angle : 0.607 8.838 20932 Z= 0.317 Chirality : 0.044 0.226 2306 Planarity : 0.005 0.056 2566 Dihedral : 18.007 178.062 2655 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.55 % Allowed : 9.65 % Favored : 88.81 % 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: 3.14 (0.19), residues: 1807 helix: 3.03 (0.13), residues: 1274 sheet: -1.61 (0.75), residues: 36 loop : -0.25 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 84 HIS 0.007 0.001 HIS D 82 PHE 0.027 0.002 PHE A 181 TYR 0.033 0.002 TYR B 208 ARG 0.006 0.001 ARG A 77 *********************** 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 163 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.761 Fit side-chains revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8317 (mtp180) REVERT: B 61 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (mtpt) REVERT: B 77 ARG cc_start: 0.6121 (tmm-80) cc_final: 0.5671 (ttt180) REVERT: B 167 SER cc_start: 0.8617 (m) cc_final: 0.8317 (t) REVERT: D 11 LEU cc_start: 0.7748 (mt) cc_final: 0.7436 (mp) REVERT: E 65 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: F 1 MET cc_start: 0.4839 (OUTLIER) cc_final: 0.3838 (ttt) REVERT: F 10 LYS cc_start: 0.3650 (OUTLIER) cc_final: 0.3447 (tttt) REVERT: G 244 MET cc_start: 0.0504 (mtt) cc_final: -0.0278 (tpp) outliers start: 25 outliers final: 11 residues processed: 153 average time/residue: 1.6345 time to fit residues: 274.5175 Evaluate side-chains 153 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 7 ILE 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 10 LYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 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 5 ASN B 121 GLN B 165 GLN C 76 GLN E 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15609 Z= 0.180 Angle : 0.512 9.573 20932 Z= 0.265 Chirality : 0.039 0.354 2306 Planarity : 0.004 0.056 2566 Dihedral : 17.350 178.985 2655 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.11 % Allowed : 10.39 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.46 (0.19), residues: 1807 helix: 3.32 (0.13), residues: 1276 sheet: -1.37 (0.69), residues: 46 loop : -0.30 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 84 HIS 0.005 0.001 HIS D 82 PHE 0.015 0.001 PHE A 181 TYR 0.019 0.001 TYR B 208 ARG 0.006 0.000 ARG A 77 *********************** 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 164 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8473 (mtpt) REVERT: B 77 ARG cc_start: 0.6057 (tmm-80) cc_final: 0.5552 (ttt180) REVERT: D 11 LEU cc_start: 0.7582 (mt) cc_final: 0.7364 (mp) REVERT: E 65 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: F 1 MET cc_start: 0.4522 (OUTLIER) cc_final: 0.3605 (ttt) REVERT: F 122 LEU cc_start: 0.2498 (OUTLIER) cc_final: 0.2197 (pp) REVERT: G 214 MET cc_start: 0.1091 (pmm) cc_final: 0.0695 (ttp) REVERT: G 244 MET cc_start: 0.0606 (mtt) cc_final: -0.0202 (tpp) outliers start: 18 outliers final: 6 residues processed: 155 average time/residue: 1.5593 time to fit residues: 266.6142 Evaluate side-chains 153 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 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 51 GLN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 214 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 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 E 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15609 Z= 0.208 Angle : 0.526 9.293 20932 Z= 0.273 Chirality : 0.039 0.230 2306 Planarity : 0.004 0.056 2566 Dihedral : 17.000 176.344 2655 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.36 % Allowed : 10.27 % Favored : 88.37 % 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: 3.43 (0.19), residues: 1807 helix: 3.30 (0.13), residues: 1276 sheet: -1.22 (0.70), residues: 46 loop : -0.32 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 84 HIS 0.005 0.001 HIS D 82 PHE 0.019 0.002 PHE A 181 TYR 0.025 0.002 TYR B 208 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8447 (mtpt) REVERT: D 11 LEU cc_start: 0.7662 (mt) cc_final: 0.7417 (mp) REVERT: E 65 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: F 1 MET cc_start: 0.4593 (OUTLIER) cc_final: 0.3635 (ttt) REVERT: G 4 ASN cc_start: 0.6983 (OUTLIER) cc_final: 0.6776 (t0) REVERT: G 214 MET cc_start: 0.1081 (pmm) cc_final: 0.0666 (ttp) REVERT: G 244 MET cc_start: 0.0499 (mtt) cc_final: -0.0280 (tpp) outliers start: 22 outliers final: 9 residues processed: 160 average time/residue: 1.5538 time to fit residues: 273.0227 Evaluate side-chains 155 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 214 MET 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 149 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15609 Z= 0.267 Angle : 0.579 10.116 20932 Z= 0.300 Chirality : 0.042 0.221 2306 Planarity : 0.004 0.055 2566 Dihedral : 17.158 176.994 2655 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.18 % Allowed : 10.76 % Favored : 88.06 % 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: 3.24 (0.19), residues: 1807 helix: 3.13 (0.13), residues: 1277 sheet: -1.21 (0.70), residues: 46 loop : -0.34 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 84 HIS 0.007 0.001 HIS D 82 PHE 0.023 0.002 PHE A 181 TYR 0.033 0.002 TYR B 208 ARG 0.006 0.001 ARG B 77 *********************** 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 163 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3814 (OUTLIER) cc_final: 0.3095 (mpp) REVERT: B 44 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8319 (mtp180) REVERT: B 61 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8485 (mtpt) REVERT: B 77 ARG cc_start: 0.6215 (tmm-80) cc_final: 0.5616 (ttt180) REVERT: D 11 LEU cc_start: 0.7695 (mt) cc_final: 0.7465 (mp) REVERT: E 65 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: F 1 MET cc_start: 0.4695 (OUTLIER) cc_final: 0.3721 (ttt) REVERT: F 12 ARG cc_start: 0.4732 (tmt170) cc_final: 0.4005 (tmt90) REVERT: G 4 ASN cc_start: 0.7017 (OUTLIER) cc_final: 0.6801 (t0) REVERT: G 106 LEU cc_start: -0.0408 (mt) cc_final: -0.0905 (tp) REVERT: G 244 MET cc_start: 0.0697 (mtt) cc_final: -0.0117 (tpp) outliers start: 19 outliers final: 11 residues processed: 152 average time/residue: 1.6124 time to fit residues: 268.6369 Evaluate side-chains 159 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 214 MET 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 103 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 141 optimal weight: 0.0000 chunk 14 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 E 171 ASN F 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15609 Z= 0.174 Angle : 0.506 10.093 20932 Z= 0.262 Chirality : 0.038 0.232 2306 Planarity : 0.004 0.056 2566 Dihedral : 16.510 173.691 2655 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.30 % Allowed : 10.88 % Favored : 87.82 % 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: 3.63 (0.19), residues: 1807 helix: 3.45 (0.13), residues: 1270 sheet: -1.52 (1.03), residues: 26 loop : -0.24 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 84 HIS 0.005 0.001 HIS A 134 PHE 0.014 0.001 PHE A 181 TYR 0.019 0.001 TYR B 208 ARG 0.005 0.000 ARG A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.3798 (OUTLIER) cc_final: 0.3066 (mpp) REVERT: D 130 GLU cc_start: 0.8066 (mp0) cc_final: 0.7236 (pm20) REVERT: E 65 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: F 1 MET cc_start: 0.4568 (OUTLIER) cc_final: 0.3614 (ttt) REVERT: F 12 ARG cc_start: 0.4710 (tmt170) cc_final: 0.3993 (tmt90) REVERT: G 4 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6741 (t0) REVERT: G 106 LEU cc_start: -0.0773 (mt) cc_final: -0.1159 (tp) REVERT: G 214 MET cc_start: 0.1104 (pmm) cc_final: 0.0797 (ttp) REVERT: G 244 MET cc_start: 0.0554 (mtt) cc_final: -0.0234 (tpp) outliers start: 21 outliers final: 9 residues processed: 158 average time/residue: 1.5355 time to fit residues: 267.2022 Evaluate side-chains 159 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 257 MET 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 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 F residue 214 MET Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.207302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121657 restraints weight = 21876.583| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.62 r_work: 0.3230 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 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 = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15609 Z= 0.207 Angle : 0.539 9.985 20932 Z= 0.277 Chirality : 0.039 0.249 2306 Planarity : 0.004 0.055 2566 Dihedral : 16.501 173.435 2655 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.99 % Allowed : 11.32 % Favored : 87.69 % 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: 3.51 (0.19), residues: 1807 helix: 3.35 (0.13), residues: 1275 sheet: -1.48 (1.05), residues: 26 loop : -0.28 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 84 HIS 0.006 0.001 HIS D 82 PHE 0.019 0.002 PHE A 181 TYR 0.026 0.002 TYR B 208 ARG 0.011 0.000 ARG B 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5999.00 seconds wall clock time: 109 minutes 50.83 seconds (6590.83 seconds total)