Starting phenix.real_space_refine on Thu Mar 13 15:26:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0f_35901/03_2025/8j0f_35901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0f_35901/03_2025/8j0f_35901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j0f_35901/03_2025/8j0f_35901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0f_35901/03_2025/8j0f_35901.map" model { file = "/net/cci-nas-00/data/ceres_data/8j0f_35901/03_2025/8j0f_35901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0f_35901/03_2025/8j0f_35901.cif" } resolution = 3.3 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= 0.001 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 P 12 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 5588 2.51 5 N 1572 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8932 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "B" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "D" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.25, per 1000 atoms: 0.59 Number of scatterers: 8932 At special positions: 0 Unit cell: (102.82, 92.22, 94.34, 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) S 36 16.00 P 12 15.00 Mg 4 11.99 O 1720 8.00 N 1572 7.00 C 5588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP C 802 " pdb=" CB RGP A 802 " pdb=" CB RGP B 802 " pdb=" CB RGP D 802 " Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 58.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'C' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY C 31 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 61 through 78 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS C 285 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'A' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY A 31 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 51 Processing helix chain 'A' and resid 61 through 78 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG A 129 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS A 285 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 79 through 85 Processing helix chain 'B' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY B 31 " --> pdb=" O GLY B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 Processing helix chain 'B' and resid 61 through 78 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS B 285 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'D' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY D 31 " --> pdb=" O GLY D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 51 Processing helix chain 'D' and resid 61 through 78 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG D 129 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 Processing helix chain 'D' and resid 175 through 187 Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS D 285 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 79 through 85 Processing sheet with id=AA1, first strand: chain 'C' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR C 117 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL C 152 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA C 119 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN C 154 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET C 121 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL C 55 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG C 16 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE C 193 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 18 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 195 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS C 20 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 192 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR C 259 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU C 194 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR A 117 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 152 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA A 119 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN A 154 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 121 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A 55 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG A 16 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE A 193 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 18 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A 195 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS A 20 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 192 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR A 259 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU A 194 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR B 117 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL B 152 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 119 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN B 154 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 121 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B 55 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG B 16 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE B 193 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 18 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 195 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 20 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 192 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR B 259 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU B 194 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR D 117 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL D 152 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA D 119 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN D 154 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET D 121 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL D 55 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG D 16 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE D 193 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL D 18 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 195 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS D 20 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 192 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR D 259 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU D 194 " --> pdb=" O THR D 259 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1788 1.32 - 1.44: 2040 1.44 - 1.56: 5136 1.56 - 1.68: 20 1.68 - 1.80: 64 Bond restraints: 9048 Sorted by residual: bond pdb=" OE2 RGP D 802 " pdb=" PA RGP D 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP A 802 " pdb=" PA RGP A 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP B 802 " pdb=" PA RGP B 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" CD RGP A 802 " pdb=" OE2 RGP A 802 " ideal model delta sigma weight residual 1.302 1.455 -0.153 2.00e-02 2.50e+03 5.86e+01 ... (remaining 9043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 11268 1.67 - 3.34: 620 3.34 - 5.01: 224 5.01 - 6.68: 80 6.68 - 8.34: 20 Bond angle restraints: 12212 Sorted by residual: angle pdb=" N ILE C 150 " pdb=" CA ILE C 150 " pdb=" C ILE C 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE B 150 " pdb=" CA ILE B 150 " pdb=" C ILE B 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE D 150 " pdb=" CA ILE D 150 " pdb=" C ILE D 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE A 150 " pdb=" CA ILE A 150 " pdb=" C ILE A 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N VAL B 254 " pdb=" CA VAL B 254 " pdb=" C VAL B 254 " ideal model delta sigma weight residual 107.55 112.76 -5.21 9.90e-01 1.02e+00 2.77e+01 ... (remaining 12207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 5260 34.62 - 69.24: 178 69.24 - 103.86: 16 103.86 - 138.48: 8 138.48 - 173.11: 2 Dihedral angle restraints: 5464 sinusoidal: 2216 harmonic: 3248 Sorted by residual: dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.10 -173.11 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.10 -173.11 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 170.94 129.07 1 2.00e+01 2.50e-03 3.91e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 972 0.043 - 0.085: 320 0.085 - 0.128: 96 0.128 - 0.170: 8 0.170 - 0.213: 12 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA MET D 110 " pdb=" N MET D 110 " pdb=" C MET D 110 " pdb=" CB MET D 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET C 110 " pdb=" N MET C 110 " pdb=" C MET C 110 " pdb=" CB MET C 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET B 110 " pdb=" N MET B 110 " pdb=" C MET B 110 " pdb=" CB MET B 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1405 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 115 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP A 115 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP A 115 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 115 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 115 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP C 115 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 115 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 115 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 115 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP D 115 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP D 115 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP D 115 " 0.013 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2014 2.77 - 3.31: 9110 3.31 - 3.84: 14972 3.84 - 4.37: 17476 4.37 - 4.90: 28944 Nonbonded interactions: 72516 Sorted by model distance: nonbonded pdb=" N GLU D 265 " pdb=" OE1 GLU D 265 " model vdw 2.242 3.120 nonbonded pdb=" N GLU B 265 " pdb=" OE1 GLU B 265 " model vdw 2.242 3.120 nonbonded pdb=" N GLU A 265 " pdb=" OE1 GLU A 265 " model vdw 2.242 3.120 nonbonded pdb=" N GLU C 265 " pdb=" OE1 GLU C 265 " model vdw 2.242 3.120 nonbonded pdb=" OD2 ASP B 208 " pdb=" OG1 THR B 210 " model vdw 2.246 3.040 ... (remaining 72511 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: 0.06 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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=1.00 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: 0.840 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.890 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.009 0.190 9048 Z= 0.639 Angle : 1.064 8.344 12212 Z= 0.653 Chirality : 0.047 0.213 1408 Planarity : 0.005 0.047 1544 Dihedral : 18.094 173.106 3368 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.13 % Allowed : 20.43 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 1108 helix: 0.35 (0.22), residues: 580 sheet: -0.20 (0.41), residues: 188 loop : 0.56 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 174 HIS 0.006 0.001 HIS B 222 PHE 0.019 0.001 PHE B 153 TYR 0.024 0.002 TYR D 106 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.120 Fit side-chains REVERT: C 68 GLN cc_start: 0.8657 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 68 GLN cc_start: 0.8651 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 68 GLN cc_start: 0.8641 (tm-30) cc_final: 0.7797 (tm-30) REVERT: D 68 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 20 outliers final: 0 residues processed: 194 average time/residue: 0.2357 time to fit residues: 60.9431 Evaluate side-chains 179 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.071601 restraints weight = 21672.907| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.05 r_work: 0.2926 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9048 Z= 0.198 Angle : 0.676 9.348 12212 Z= 0.326 Chirality : 0.042 0.142 1408 Planarity : 0.003 0.023 1544 Dihedral : 13.507 178.735 1300 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.28 % Allowed : 19.89 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1108 helix: 1.08 (0.21), residues: 596 sheet: 0.02 (0.41), residues: 188 loop : 0.85 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 287 HIS 0.003 0.001 HIS C 222 PHE 0.022 0.002 PHE F 80 TYR 0.023 0.002 TYR D 106 ARG 0.002 0.000 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.937 Fit side-chains REVERT: C 80 PHE cc_start: 0.9387 (t80) cc_final: 0.9145 (t80) REVERT: C 115 ASP cc_start: 0.8944 (t0) cc_final: 0.8741 (t0) REVERT: C 186 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8329 (tm-30) REVERT: C 228 PHE cc_start: 0.8310 (m-10) cc_final: 0.8089 (m-10) REVERT: A 115 ASP cc_start: 0.8944 (t0) cc_final: 0.8732 (t0) REVERT: A 131 LYS cc_start: 0.9235 (pttm) cc_final: 0.8958 (mmmt) REVERT: A 228 PHE cc_start: 0.8281 (m-10) cc_final: 0.8046 (m-10) REVERT: B 54 GLU cc_start: 0.8686 (mp0) cc_final: 0.8028 (pm20) REVERT: B 115 ASP cc_start: 0.8973 (t0) cc_final: 0.8747 (t0) REVERT: B 132 ASP cc_start: 0.8874 (t0) cc_final: 0.8599 (t0) REVERT: B 157 ASP cc_start: 0.8751 (m-30) cc_final: 0.8549 (m-30) REVERT: B 220 GLU cc_start: 0.9480 (tp30) cc_final: 0.9156 (tm-30) REVERT: B 239 MET cc_start: 0.8857 (tpp) cc_final: 0.7421 (tpp) REVERT: B 251 TYR cc_start: 0.8649 (m-80) cc_final: 0.8315 (m-80) REVERT: D 115 ASP cc_start: 0.8933 (t0) cc_final: 0.8721 (t0) REVERT: D 132 ASP cc_start: 0.8900 (t0) cc_final: 0.8645 (t0) REVERT: D 157 ASP cc_start: 0.8762 (m-30) cc_final: 0.8546 (m-30) REVERT: D 186 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8339 (tm-30) REVERT: D 251 TYR cc_start: 0.8684 (m-80) cc_final: 0.8362 (m-80) outliers start: 12 outliers final: 4 residues processed: 206 average time/residue: 0.2233 time to fit residues: 61.9165 Evaluate side-chains 177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 64 optimal weight: 0.0670 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.067257 restraints weight = 22064.525| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.29 r_work: 0.2855 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9048 Z= 0.203 Angle : 0.633 11.278 12212 Z= 0.303 Chirality : 0.040 0.136 1408 Planarity : 0.003 0.024 1544 Dihedral : 12.548 158.848 1300 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.66 % Allowed : 20.00 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1108 helix: 1.46 (0.21), residues: 596 sheet: 0.17 (0.41), residues: 188 loop : 0.88 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 287 HIS 0.003 0.001 HIS C 222 PHE 0.027 0.002 PHE E 80 TYR 0.031 0.002 TYR C 106 ARG 0.002 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: C 115 ASP cc_start: 0.8986 (t0) cc_final: 0.8697 (t0) REVERT: C 121 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8017 (mmm) REVERT: C 186 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8498 (tm-30) REVERT: C 239 MET cc_start: 0.8277 (mmm) cc_final: 0.7851 (ttm) REVERT: F 80 PHE cc_start: 0.8595 (t80) cc_final: 0.8379 (t80) REVERT: A 110 MET cc_start: 0.8688 (mtt) cc_final: 0.8288 (mtm) REVERT: A 115 ASP cc_start: 0.9000 (t0) cc_final: 0.8711 (t0) REVERT: A 121 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8084 (mmm) REVERT: A 186 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8480 (tm-30) REVERT: A 239 MET cc_start: 0.8266 (mmm) cc_final: 0.7871 (ttm) REVERT: E 80 PHE cc_start: 0.8652 (t80) cc_final: 0.8408 (t80) REVERT: B 83 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9136 (mp) REVERT: B 115 ASP cc_start: 0.8971 (t0) cc_final: 0.8691 (t0) REVERT: B 121 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.7991 (mmm) REVERT: B 239 MET cc_start: 0.8728 (tpp) cc_final: 0.7100 (tpp) REVERT: D 115 ASP cc_start: 0.8955 (t0) cc_final: 0.8683 (t0) REVERT: D 121 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.7979 (mmm) REVERT: D 186 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8504 (tm-30) REVERT: D 239 MET cc_start: 0.8409 (mmm) cc_final: 0.7884 (ttm) REVERT: H 80 PHE cc_start: 0.8651 (t80) cc_final: 0.8423 (t80) outliers start: 25 outliers final: 6 residues processed: 201 average time/residue: 0.2270 time to fit residues: 61.5808 Evaluate side-chains 186 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 72 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 248 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 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 = 0.3368 r_free = 0.3368 target = 0.086247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065254 restraints weight = 22175.894| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.17 r_work: 0.2766 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9048 Z= 0.249 Angle : 0.630 6.840 12212 Z= 0.301 Chirality : 0.041 0.146 1408 Planarity : 0.003 0.026 1544 Dihedral : 11.650 135.137 1300 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.62 % Allowed : 21.06 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1108 helix: 1.65 (0.21), residues: 596 sheet: 0.13 (0.40), residues: 188 loop : 1.12 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 174 HIS 0.002 0.001 HIS A 222 PHE 0.025 0.002 PHE A 80 TYR 0.027 0.002 TYR D 106 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 1.078 Fit side-chains REVERT: C 83 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9170 (mp) REVERT: C 115 ASP cc_start: 0.8989 (t0) cc_final: 0.8710 (t0) REVERT: C 121 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8147 (mmm) REVERT: C 132 ASP cc_start: 0.9448 (m-30) cc_final: 0.8782 (t0) REVERT: C 239 MET cc_start: 0.8490 (mmm) cc_final: 0.7946 (tpp) REVERT: F 80 PHE cc_start: 0.8741 (t80) cc_final: 0.8423 (t80) REVERT: A 83 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9081 (mp) REVERT: A 115 ASP cc_start: 0.8972 (t0) cc_final: 0.8697 (t0) REVERT: A 121 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8202 (mmm) REVERT: A 239 MET cc_start: 0.8448 (mmm) cc_final: 0.7940 (tpp) REVERT: A 287 TRP cc_start: 0.7719 (m-10) cc_final: 0.7502 (m-10) REVERT: E 80 PHE cc_start: 0.8705 (t80) cc_final: 0.8327 (t80) REVERT: B 54 GLU cc_start: 0.8481 (mp0) cc_final: 0.7724 (pm20) REVERT: B 89 GLU cc_start: 0.8847 (tp30) cc_final: 0.8638 (tp30) REVERT: B 115 ASP cc_start: 0.8982 (t0) cc_final: 0.8720 (t0) REVERT: B 121 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8087 (mmm) REVERT: B 220 GLU cc_start: 0.9683 (tp30) cc_final: 0.9394 (tm-30) REVERT: B 239 MET cc_start: 0.8750 (tpp) cc_final: 0.7141 (tpp) REVERT: B 248 ASN cc_start: 0.9214 (t0) cc_final: 0.9011 (t0) REVERT: B 287 TRP cc_start: 0.7711 (m-10) cc_final: 0.7490 (m-10) REVERT: D 83 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9166 (mp) REVERT: D 110 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8293 (mtm) REVERT: D 115 ASP cc_start: 0.8966 (t0) cc_final: 0.8687 (t0) REVERT: D 121 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8033 (mmm) REVERT: D 239 MET cc_start: 0.8369 (mmm) cc_final: 0.7706 (ttm) outliers start: 34 outliers final: 16 residues processed: 202 average time/residue: 0.2179 time to fit residues: 59.7532 Evaluate side-chains 192 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.066244 restraints weight = 22814.011| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.22 r_work: 0.2843 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9048 Z= 0.232 Angle : 0.632 9.792 12212 Z= 0.300 Chirality : 0.040 0.139 1408 Planarity : 0.003 0.026 1544 Dihedral : 11.131 134.899 1300 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.83 % Allowed : 21.60 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.26), residues: 1108 helix: 1.68 (0.21), residues: 596 sheet: 0.14 (0.40), residues: 188 loop : 1.26 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 287 HIS 0.002 0.001 HIS C 222 PHE 0.018 0.001 PHE H 80 TYR 0.029 0.002 TYR C 106 ARG 0.001 0.000 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: C 68 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8736 (tm-30) REVERT: C 115 ASP cc_start: 0.9044 (t0) cc_final: 0.8765 (t0) REVERT: C 121 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: C 132 ASP cc_start: 0.9430 (m-30) cc_final: 0.8740 (t0) REVERT: C 239 MET cc_start: 0.8612 (mmm) cc_final: 0.8023 (tpp) REVERT: A 110 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8247 (mtp) REVERT: A 115 ASP cc_start: 0.9010 (t0) cc_final: 0.8721 (t0) REVERT: A 121 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8278 (mmm) REVERT: A 239 MET cc_start: 0.8568 (mmm) cc_final: 0.8022 (tpp) REVERT: A 251 TYR cc_start: 0.8734 (m-80) cc_final: 0.8352 (m-80) REVERT: A 287 TRP cc_start: 0.7888 (m-10) cc_final: 0.7577 (m-10) REVERT: E 80 PHE cc_start: 0.8821 (t80) cc_final: 0.8593 (t80) REVERT: B 89 GLU cc_start: 0.8937 (tp30) cc_final: 0.8736 (tp30) REVERT: B 115 ASP cc_start: 0.8983 (t0) cc_final: 0.8698 (t0) REVERT: B 121 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8150 (mmm) REVERT: B 239 MET cc_start: 0.8893 (tpp) cc_final: 0.7278 (tpp) REVERT: B 251 TYR cc_start: 0.8743 (m-80) cc_final: 0.8362 (m-80) REVERT: B 287 TRP cc_start: 0.7847 (m-10) cc_final: 0.7529 (m-10) REVERT: D 68 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8727 (tm-30) REVERT: D 83 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9144 (mp) REVERT: D 115 ASP cc_start: 0.8985 (t0) cc_final: 0.8694 (t0) REVERT: D 121 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8171 (mmm) REVERT: D 239 MET cc_start: 0.8517 (mmm) cc_final: 0.7822 (ttm) REVERT: D 251 TYR cc_start: 0.8778 (m-80) cc_final: 0.8431 (m-80) outliers start: 36 outliers final: 12 residues processed: 188 average time/residue: 0.2421 time to fit residues: 62.5553 Evaluate side-chains 183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.086836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.065180 restraints weight = 23331.699| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.31 r_work: 0.2813 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9048 Z= 0.278 Angle : 0.653 11.537 12212 Z= 0.309 Chirality : 0.041 0.158 1408 Planarity : 0.003 0.028 1544 Dihedral : 10.894 134.437 1300 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.15 % Allowed : 21.38 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.26), residues: 1108 helix: 1.70 (0.21), residues: 596 sheet: 0.07 (0.39), residues: 188 loop : 1.33 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 287 HIS 0.002 0.001 HIS D 222 PHE 0.025 0.002 PHE G 80 TYR 0.018 0.002 TYR C 106 ARG 0.001 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 PHE cc_start: 0.9420 (t80) cc_final: 0.9216 (t80) REVERT: C 115 ASP cc_start: 0.9055 (t0) cc_final: 0.8769 (t0) REVERT: C 121 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8241 (mmm) REVERT: C 132 ASP cc_start: 0.9445 (m-30) cc_final: 0.8806 (t0) REVERT: C 239 MET cc_start: 0.8748 (mmm) cc_final: 0.8104 (tpp) REVERT: C 251 TYR cc_start: 0.8723 (m-80) cc_final: 0.8348 (m-80) REVERT: A 115 ASP cc_start: 0.9031 (t0) cc_final: 0.8749 (t0) REVERT: A 121 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8311 (mmm) REVERT: A 239 MET cc_start: 0.8712 (mmm) cc_final: 0.8098 (tpp) REVERT: A 251 TYR cc_start: 0.8752 (m-80) cc_final: 0.8404 (m-80) REVERT: E 80 PHE cc_start: 0.8812 (t80) cc_final: 0.8582 (t80) REVERT: B 68 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8821 (tm-30) REVERT: B 115 ASP cc_start: 0.9010 (t0) cc_final: 0.8739 (t0) REVERT: B 121 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8138 (mmm) REVERT: B 251 TYR cc_start: 0.8774 (m-80) cc_final: 0.8385 (m-80) REVERT: B 287 TRP cc_start: 0.8139 (m-10) cc_final: 0.7695 (m-10) REVERT: D 83 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9055 (mp) REVERT: D 115 ASP cc_start: 0.9000 (t0) cc_final: 0.8740 (t0) REVERT: D 121 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: D 239 MET cc_start: 0.8677 (mmm) cc_final: 0.7953 (ttm) outliers start: 39 outliers final: 18 residues processed: 191 average time/residue: 0.2548 time to fit residues: 66.6114 Evaluate side-chains 188 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.088111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067059 restraints weight = 23469.155| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.30 r_work: 0.2861 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9048 Z= 0.199 Angle : 0.642 8.487 12212 Z= 0.302 Chirality : 0.040 0.132 1408 Planarity : 0.003 0.030 1544 Dihedral : 10.403 132.742 1300 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.09 % Allowed : 23.51 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.99 (0.27), residues: 1108 helix: 1.77 (0.22), residues: 596 sheet: 0.15 (0.39), residues: 188 loop : 1.50 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 287 HIS 0.001 0.000 HIS C 222 PHE 0.029 0.002 PHE A 80 TYR 0.022 0.002 TYR A 106 ARG 0.001 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: C 68 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8812 (tm-30) REVERT: C 87 GLN cc_start: 0.9044 (pm20) cc_final: 0.8833 (pm20) REVERT: C 110 MET cc_start: 0.8248 (mpp) cc_final: 0.7989 (mtt) REVERT: C 115 ASP cc_start: 0.8965 (t0) cc_final: 0.8689 (t0) REVERT: C 121 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8285 (mmm) REVERT: C 132 ASP cc_start: 0.9387 (m-30) cc_final: 0.8771 (t0) REVERT: C 239 MET cc_start: 0.8762 (mmm) cc_final: 0.8196 (tpp) REVERT: C 251 TYR cc_start: 0.8726 (m-80) cc_final: 0.8388 (m-80) REVERT: A 115 ASP cc_start: 0.8979 (t0) cc_final: 0.8692 (t0) REVERT: A 121 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8281 (mmm) REVERT: A 239 MET cc_start: 0.8734 (mmm) cc_final: 0.8209 (tpp) REVERT: A 251 TYR cc_start: 0.8758 (m-80) cc_final: 0.8367 (m-80) REVERT: E 80 PHE cc_start: 0.8813 (t80) cc_final: 0.8609 (t80) REVERT: B 38 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8940 (mp) REVERT: B 115 ASP cc_start: 0.8966 (t0) cc_final: 0.8708 (t0) REVERT: B 121 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8164 (mmm) REVERT: B 239 MET cc_start: 0.9074 (tpp) cc_final: 0.7549 (tpp) REVERT: B 287 TRP cc_start: 0.8114 (m-10) cc_final: 0.7611 (m-10) REVERT: D 83 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9090 (mp) REVERT: D 115 ASP cc_start: 0.8986 (t0) cc_final: 0.8709 (t0) REVERT: D 121 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8192 (mmm) REVERT: D 239 MET cc_start: 0.8674 (mmm) cc_final: 0.8145 (tpp) REVERT: D 251 TYR cc_start: 0.8681 (m-80) cc_final: 0.8360 (m-80) outliers start: 29 outliers final: 15 residues processed: 180 average time/residue: 0.2286 time to fit residues: 55.4849 Evaluate side-chains 186 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.066253 restraints weight = 23258.062| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.21 r_work: 0.2859 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9048 Z= 0.214 Angle : 0.660 9.439 12212 Z= 0.313 Chirality : 0.040 0.205 1408 Planarity : 0.003 0.030 1544 Dihedral : 10.079 130.600 1300 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.30 % Allowed : 23.30 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.06 (0.27), residues: 1108 helix: 1.83 (0.22), residues: 596 sheet: 0.21 (0.39), residues: 188 loop : 1.50 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 287 HIS 0.001 0.000 HIS C 222 PHE 0.025 0.002 PHE G 80 TYR 0.027 0.002 TYR A 106 ARG 0.003 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: C 87 GLN cc_start: 0.9063 (pm20) cc_final: 0.8845 (pm20) REVERT: C 115 ASP cc_start: 0.8972 (t0) cc_final: 0.8696 (t0) REVERT: C 121 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8285 (mmm) REVERT: C 132 ASP cc_start: 0.9368 (m-30) cc_final: 0.8755 (t0) REVERT: C 186 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8593 (tm-30) REVERT: C 219 LYS cc_start: 0.8593 (mttt) cc_final: 0.8349 (mtmt) REVERT: C 239 MET cc_start: 0.8809 (mmm) cc_final: 0.8307 (tpp) REVERT: A 115 ASP cc_start: 0.9029 (t0) cc_final: 0.8721 (t0) REVERT: A 121 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8319 (mmm) REVERT: A 239 MET cc_start: 0.8765 (mmm) cc_final: 0.8339 (tpp) REVERT: B 38 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8953 (mp) REVERT: B 115 ASP cc_start: 0.8943 (t0) cc_final: 0.8691 (t0) REVERT: B 121 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8187 (mmm) REVERT: B 239 MET cc_start: 0.9117 (tpp) cc_final: 0.7598 (tpp) REVERT: B 287 TRP cc_start: 0.8226 (m-10) cc_final: 0.7946 (m-10) REVERT: D 115 ASP cc_start: 0.8970 (t0) cc_final: 0.8707 (t0) REVERT: D 121 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8231 (mmm) REVERT: D 186 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8589 (tm-30) REVERT: D 239 MET cc_start: 0.8733 (mmm) cc_final: 0.8171 (tpp) REVERT: D 251 TYR cc_start: 0.8675 (m-80) cc_final: 0.8349 (m-80) outliers start: 31 outliers final: 14 residues processed: 180 average time/residue: 0.2560 time to fit residues: 63.4410 Evaluate side-chains 183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.086384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.065322 restraints weight = 23237.094| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.14 r_work: 0.2830 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9048 Z= 0.265 Angle : 0.680 8.244 12212 Z= 0.323 Chirality : 0.041 0.323 1408 Planarity : 0.003 0.031 1544 Dihedral : 9.953 127.695 1300 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.66 % Allowed : 24.26 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.27), residues: 1108 helix: 1.86 (0.22), residues: 596 sheet: 0.15 (0.38), residues: 188 loop : 1.48 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 287 HIS 0.002 0.001 HIS B 222 PHE 0.028 0.002 PHE E 80 TYR 0.039 0.002 TYR A 106 ARG 0.002 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 ASP cc_start: 0.8971 (t0) cc_final: 0.8684 (t0) REVERT: C 121 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8305 (mmm) REVERT: C 132 ASP cc_start: 0.9388 (m-30) cc_final: 0.8801 (t0) REVERT: C 186 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8592 (tm-30) REVERT: C 239 MET cc_start: 0.8919 (mmm) cc_final: 0.8360 (tpp) REVERT: C 251 TYR cc_start: 0.8672 (m-80) cc_final: 0.8354 (m-80) REVERT: A 115 ASP cc_start: 0.9030 (t0) cc_final: 0.8730 (t0) REVERT: A 121 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8311 (mmm) REVERT: A 219 LYS cc_start: 0.8730 (mttt) cc_final: 0.8451 (mttt) REVERT: A 239 MET cc_start: 0.8897 (mmm) cc_final: 0.8200 (ttm) REVERT: A 251 TYR cc_start: 0.8674 (m-80) cc_final: 0.8261 (m-80) REVERT: B 38 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8961 (mp) REVERT: B 115 ASP cc_start: 0.8930 (t0) cc_final: 0.8655 (t0) REVERT: B 121 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8208 (mmm) REVERT: B 251 TYR cc_start: 0.8694 (m-80) cc_final: 0.8369 (m-80) REVERT: D 115 ASP cc_start: 0.8988 (t0) cc_final: 0.8710 (t0) REVERT: D 121 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8253 (mmm) REVERT: D 186 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 239 MET cc_start: 0.8807 (mmm) cc_final: 0.8012 (ttm) outliers start: 25 outliers final: 15 residues processed: 177 average time/residue: 0.2299 time to fit residues: 55.0921 Evaluate side-chains 186 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 0.0270 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.088174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.067378 restraints weight = 23023.793| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.17 r_work: 0.2874 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9048 Z= 0.209 Angle : 0.689 8.436 12212 Z= 0.328 Chirality : 0.040 0.171 1408 Planarity : 0.003 0.029 1544 Dihedral : 9.659 126.169 1300 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.13 % Allowed : 25.64 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.26), residues: 1108 helix: 2.12 (0.22), residues: 572 sheet: 0.58 (0.39), residues: 180 loop : 1.42 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 287 HIS 0.006 0.001 HIS C 222 PHE 0.027 0.001 PHE G 80 TYR 0.031 0.002 TYR A 106 ARG 0.002 0.000 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 ASP cc_start: 0.8964 (t0) cc_final: 0.8685 (t0) REVERT: C 121 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8300 (mmm) REVERT: C 132 ASP cc_start: 0.9359 (m-30) cc_final: 0.8791 (t0) REVERT: C 186 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8565 (tm-30) REVERT: C 239 MET cc_start: 0.8880 (mmm) cc_final: 0.8414 (tpp) REVERT: C 251 TYR cc_start: 0.8668 (m-80) cc_final: 0.8343 (m-80) REVERT: A 115 ASP cc_start: 0.8944 (t0) cc_final: 0.8652 (t0) REVERT: A 121 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8335 (mmm) REVERT: A 239 MET cc_start: 0.8859 (mmm) cc_final: 0.8428 (tpp) REVERT: A 251 TYR cc_start: 0.8645 (m-80) cc_final: 0.8290 (m-80) REVERT: B 38 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8942 (mp) REVERT: B 115 ASP cc_start: 0.8913 (t0) cc_final: 0.8651 (t0) REVERT: B 121 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8195 (mmm) REVERT: B 239 MET cc_start: 0.9154 (tpp) cc_final: 0.7716 (tpp) REVERT: B 251 TYR cc_start: 0.8676 (m-80) cc_final: 0.8347 (m-80) REVERT: D 115 ASP cc_start: 0.8964 (t0) cc_final: 0.8704 (t0) REVERT: D 121 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8229 (mmm) REVERT: D 186 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8573 (tm-30) REVERT: D 239 MET cc_start: 0.8739 (mmm) cc_final: 0.8212 (tpp) REVERT: D 251 TYR cc_start: 0.8697 (m-80) cc_final: 0.8363 (m-80) outliers start: 20 outliers final: 14 residues processed: 177 average time/residue: 0.2212 time to fit residues: 53.3861 Evaluate side-chains 182 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067258 restraints weight = 23132.826| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.20 r_work: 0.2873 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9048 Z= 0.210 Angle : 0.674 8.041 12212 Z= 0.318 Chirality : 0.040 0.132 1408 Planarity : 0.003 0.027 1544 Dihedral : 9.317 123.937 1300 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.13 % Allowed : 25.21 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.26), residues: 1108 helix: 2.18 (0.22), residues: 572 sheet: 0.62 (0.39), residues: 180 loop : 1.44 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 287 HIS 0.001 0.000 HIS B 222 PHE 0.029 0.002 PHE E 80 TYR 0.036 0.002 TYR C 106 ARG 0.004 0.000 ARG D 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3967.21 seconds wall clock time: 70 minutes 45.92 seconds (4245.92 seconds total)