Starting phenix.real_space_refine on Thu Mar 13 06:49:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wx3_32875/03_2025/7wx3_32875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wx3_32875/03_2025/7wx3_32875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wx3_32875/03_2025/7wx3_32875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wx3_32875/03_2025/7wx3_32875.map" model { file = "/net/cci-nas-00/data/ceres_data/7wx3_32875/03_2025/7wx3_32875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wx3_32875/03_2025/7wx3_32875.cif" } resolution = 3.1 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= 0.006 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 68 5.16 5 C 5296 2.51 5 N 1429 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 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: 8472 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1930 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 3 Chain: "E" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 113 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1974 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 3 Chain: "F" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 113 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "C" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1974 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 3 Chain: "G" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 113 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1974 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 3 Chain: "H" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 113 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.25, per 1000 atoms: 0.74 Number of scatterers: 8472 At special positions: 0 Unit cell: (104.94, 92.22, 100.7, 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 68 16.00 P 12 15.00 Mg 4 11.99 O 1663 8.00 N 1429 7.00 C 5296 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP A 801 " pdb=" CB RGP B 801 " pdb=" CB RGP C 801 " pdb=" CB RGP D 801 " Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 49.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.548A pdb=" N LEU A 53 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 93 Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.632A pdb=" N PHE A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.715A pdb=" N LEU A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 163 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.945A pdb=" N LEU E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 56 removed outlier: 3.548A pdb=" N LEU B 53 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.609A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.715A pdb=" N LEU B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.926A pdb=" N SER B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.945A pdb=" N LEU F 127 " --> pdb=" O MET F 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.532A pdb=" N LEU C 53 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 93 Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.633A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.725A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 163 Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.915A pdb=" N SER C 281 " --> pdb=" O ASP C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 308 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.945A pdb=" N LEU G 127 " --> pdb=" O MET G 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 56 removed outlier: 3.530A pdb=" N LEU D 53 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.633A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.726A pdb=" N LEU D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 163 Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 276 through 282 removed outlier: 3.897A pdb=" N SER D 281 " --> pdb=" O ASP D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'H' and resid 122 through 127 removed outlier: 3.945A pdb=" N LEU H 127 " --> pdb=" O MET H 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 173 removed outlier: 6.599A pdb=" N ALA A 169 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASN A 204 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 171 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET A 100 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N THR A 205 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL A 101 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 61 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU A 249 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N CYS A 315 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 251 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR A 274 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.608A pdb=" N ALA B 169 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN B 204 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 171 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET B 100 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N THR B 205 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL B 101 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 61 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B 249 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N CYS B 315 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 251 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 312 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 337 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.618A pdb=" N ALA C 169 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN C 204 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL C 171 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N MET C 100 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N THR C 205 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 101 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 61 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU C 249 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N CYS C 315 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C 251 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 312 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 337 " --> pdb=" O TYR C 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 168 through 173 removed outlier: 6.612A pdb=" N ALA D 169 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASN D 204 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL D 171 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET D 100 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N THR D 205 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL D 101 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL D 61 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU D 249 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N CYS D 315 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU D 251 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 312 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 337 " --> pdb=" O TYR D 274 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1002 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: 2.45 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1437 1.31 - 1.43: 1980 1.43 - 1.55: 5011 1.55 - 1.68: 20 1.68 - 1.80: 124 Bond restraints: 8572 Sorted by residual: bond pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " ideal model delta sigma weight residual 1.798 1.647 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" OE2 RGP D 801 " pdb=" PA RGP D 801 " ideal model delta sigma weight residual 1.798 1.647 0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" OE2 RGP B 801 " pdb=" PA RGP B 801 " ideal model delta sigma weight residual 1.798 1.647 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" OE2 RGP C 801 " pdb=" PA RGP C 801 " ideal model delta sigma weight residual 1.798 1.647 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD RGP D 801 " pdb=" OE2 RGP D 801 " ideal model delta sigma weight residual 1.302 1.399 -0.097 2.00e-02 2.50e+03 2.37e+01 ... (remaining 8567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 11374 2.52 - 5.05: 146 5.05 - 7.57: 44 7.57 - 10.10: 8 10.10 - 12.62: 12 Bond angle restraints: 11584 Sorted by residual: angle pdb=" O1B ADP A 802 " pdb=" PB ADP A 802 " pdb=" O3B ADP A 802 " ideal model delta sigma weight residual 119.90 107.28 12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O1B ADP B 802 " pdb=" PB ADP B 802 " pdb=" O3B ADP B 802 " ideal model delta sigma weight residual 119.90 107.29 12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O1B ADP D 802 " pdb=" PB ADP D 802 " pdb=" O2B ADP D 802 " ideal model delta sigma weight residual 119.90 107.32 12.58 3.00e+00 1.11e-01 1.76e+01 angle pdb=" O1B ADP C 802 " pdb=" PB ADP C 802 " pdb=" O2B ADP C 802 " ideal model delta sigma weight residual 119.90 107.32 12.58 3.00e+00 1.11e-01 1.76e+01 angle pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " pdb=" OA3 RGP A 801 " ideal model delta sigma weight residual 97.78 109.45 -11.67 3.00e+00 1.11e-01 1.51e+01 ... (remaining 11579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.56: 5060 31.56 - 63.11: 176 63.11 - 94.67: 6 94.67 - 126.22: 6 126.22 - 157.78: 4 Dihedral angle restraints: 5252 sinusoidal: 2130 harmonic: 3122 Sorted by residual: dihedral pdb=" O1B ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " pdb=" PA ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 97.77 -157.78 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" O1B ADP B 802 " pdb=" O3A ADP B 802 " pdb=" PB ADP B 802 " pdb=" PA ADP B 802 " ideal model delta sinusoidal sigma weight residual -60.00 97.34 -157.35 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O2A ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PA ADP A 802 " pdb=" PB ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 70.54 -130.54 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 547 0.029 - 0.057: 508 0.057 - 0.086: 211 0.086 - 0.114: 92 0.114 - 0.143: 15 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ILE B 199 " pdb=" N ILE B 199 " pdb=" C ILE B 199 " pdb=" CB ILE B 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE D 199 " pdb=" N ILE D 199 " pdb=" C ILE D 199 " pdb=" CB ILE D 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1370 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 175 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO A 176 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 175 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO D 176 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 176 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 175 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO C 176 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 176 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 176 " -0.021 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 291 2.70 - 3.25: 8163 3.25 - 3.80: 12487 3.80 - 4.35: 16058 4.35 - 4.90: 28672 Nonbonded interactions: 65671 Sorted by model distance: nonbonded pdb=" O THR D 275 " pdb=" OG SER D 279 " model vdw 2.150 3.040 nonbonded pdb=" OA3 RGP A 801 " pdb="MG MG A 803 " model vdw 2.152 2.170 nonbonded pdb=" OA3 RGP D 801 " pdb="MG MG D 803 " model vdw 2.154 2.170 nonbonded pdb=" OA3 RGP B 801 " pdb="MG MG B 803 " model vdw 2.166 2.170 nonbonded pdb=" OA3 RGP C 801 " pdb="MG MG C 803 " model vdw 2.171 2.170 ... (remaining 65666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 45 through 276 or resid 295 through 338 or resid 801 or re \ sid 802 through 803)) selection = (chain 'C' and (resid 45 through 276 or resid 295 through 338 or resid 801 or re \ sid 802 through 803)) selection = (chain 'D' and (resid 45 through 276 or resid 295 through 338 or resid 801 or re \ sid 802 through 803)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.560 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.650 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.011 0.151 8572 Z= 0.722 Angle : 0.914 12.622 11584 Z= 0.425 Chirality : 0.048 0.143 1373 Planarity : 0.004 0.039 1447 Dihedral : 16.740 157.776 3216 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.70 % Allowed : 16.99 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.23), residues: 1042 helix: -1.50 (0.21), residues: 526 sheet: -3.17 (0.31), residues: 156 loop : -2.96 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 264 HIS 0.004 0.001 HIS D 92 PHE 0.010 0.002 PHE A 335 TYR 0.014 0.002 TYR A 274 ARG 0.002 0.000 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8867 (mttt) cc_final: 0.8645 (mtmm) REVERT: A 57 ARG cc_start: 0.7872 (tpt170) cc_final: 0.7573 (mmp-170) REVERT: A 94 GLU cc_start: 0.8240 (tt0) cc_final: 0.7637 (tm-30) REVERT: A 118 LEU cc_start: 0.7847 (tp) cc_final: 0.7605 (tp) REVERT: A 247 ASP cc_start: 0.8065 (m-30) cc_final: 0.7434 (m-30) REVERT: A 274 TYR cc_start: 0.8453 (t80) cc_final: 0.8199 (t80) REVERT: B 57 ARG cc_start: 0.7871 (tpt170) cc_final: 0.7597 (mmp-170) REVERT: B 94 GLU cc_start: 0.8214 (tt0) cc_final: 0.7641 (tm-30) REVERT: B 118 LEU cc_start: 0.7849 (tp) cc_final: 0.7607 (tp) REVERT: B 245 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8165 (mm-40) REVERT: B 247 ASP cc_start: 0.8067 (m-30) cc_final: 0.7449 (m-30) REVERT: B 274 TYR cc_start: 0.8112 (t80) cc_final: 0.7738 (t80) REVERT: C 57 ARG cc_start: 0.7849 (tpt170) cc_final: 0.7606 (mmp-170) REVERT: C 94 GLU cc_start: 0.8244 (tt0) cc_final: 0.7636 (tm-30) REVERT: C 118 LEU cc_start: 0.7850 (tp) cc_final: 0.7616 (tp) REVERT: C 247 ASP cc_start: 0.8067 (m-30) cc_final: 0.7425 (m-30) REVERT: C 274 TYR cc_start: 0.8107 (t80) cc_final: 0.7728 (t80) REVERT: D 57 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7558 (mmp-170) REVERT: D 94 GLU cc_start: 0.8247 (tt0) cc_final: 0.7630 (tm-30) REVERT: D 118 LEU cc_start: 0.7852 (tp) cc_final: 0.7616 (tp) REVERT: D 247 ASP cc_start: 0.8052 (m-30) cc_final: 0.7415 (m-30) REVERT: D 274 TYR cc_start: 0.8057 (t80) cc_final: 0.7681 (t80) outliers start: 34 outliers final: 27 residues processed: 206 average time/residue: 0.2062 time to fit residues: 58.3322 Evaluate side-chains 184 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 170 GLN C 52 GLN C 170 GLN D 52 GLN D 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.154479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112125 restraints weight = 8639.151| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.70 r_work: 0.3165 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8572 Z= 0.219 Angle : 0.575 6.207 11584 Z= 0.262 Chirality : 0.042 0.128 1373 Planarity : 0.003 0.024 1447 Dihedral : 11.935 131.050 1244 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.20 % Allowed : 20.37 % Favored : 78.43 % 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: -2.24 (0.25), residues: 1042 helix: -0.44 (0.23), residues: 528 sheet: -2.80 (0.33), residues: 156 loop : -2.28 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 304 HIS 0.001 0.001 HIS C 92 PHE 0.009 0.001 PHE B 335 TYR 0.007 0.001 TYR C 274 ARG 0.002 0.000 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8212 (mt0) cc_final: 0.7925 (mt0) REVERT: A 57 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7668 (mmp-170) REVERT: A 94 GLU cc_start: 0.8677 (tt0) cc_final: 0.7804 (tm-30) REVERT: A 177 ASP cc_start: 0.7671 (m-30) cc_final: 0.6700 (t0) REVERT: A 247 ASP cc_start: 0.8277 (m-30) cc_final: 0.7659 (m-30) REVERT: A 308 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7277 (tpp-160) REVERT: B 52 GLN cc_start: 0.8203 (mt0) cc_final: 0.7930 (mt0) REVERT: B 57 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7665 (mmp-170) REVERT: B 94 GLU cc_start: 0.8686 (tt0) cc_final: 0.7806 (tm-30) REVERT: B 177 ASP cc_start: 0.7674 (m-30) cc_final: 0.6703 (t0) REVERT: B 247 ASP cc_start: 0.8286 (m-30) cc_final: 0.7672 (m-30) REVERT: B 308 ARG cc_start: 0.7539 (tpp-160) cc_final: 0.7233 (tpp-160) REVERT: C 57 ARG cc_start: 0.8293 (tpt170) cc_final: 0.7673 (mmp-170) REVERT: C 94 GLU cc_start: 0.8699 (tt0) cc_final: 0.7799 (tm-30) REVERT: C 177 ASP cc_start: 0.7673 (m-30) cc_final: 0.6714 (t0) REVERT: C 247 ASP cc_start: 0.8277 (m-30) cc_final: 0.7654 (m-30) REVERT: C 308 ARG cc_start: 0.7519 (tpp-160) cc_final: 0.7206 (tpp-160) REVERT: D 57 ARG cc_start: 0.8275 (tpt170) cc_final: 0.7643 (mmp-170) REVERT: D 94 GLU cc_start: 0.8667 (tt0) cc_final: 0.7766 (tm-30) REVERT: D 177 ASP cc_start: 0.7675 (m-30) cc_final: 0.6702 (t0) REVERT: D 247 ASP cc_start: 0.8277 (m-30) cc_final: 0.7654 (m-30) REVERT: D 308 ARG cc_start: 0.7540 (tpp-160) cc_final: 0.7260 (tpp-160) outliers start: 11 outliers final: 5 residues processed: 179 average time/residue: 0.2105 time to fit residues: 52.1154 Evaluate side-chains 167 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 198 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112152 restraints weight = 8730.865| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.76 r_work: 0.3186 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8572 Z= 0.210 Angle : 0.562 6.336 11584 Z= 0.252 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.026 1447 Dihedral : 10.748 131.867 1210 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.72 % Allowed : 18.85 % Favored : 78.43 % 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: -1.75 (0.26), residues: 1042 helix: -0.05 (0.24), residues: 532 sheet: -2.61 (0.34), residues: 156 loop : -2.02 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 304 HIS 0.002 0.000 HIS D 92 PHE 0.014 0.001 PHE A 188 TYR 0.007 0.001 TYR C 274 ARG 0.002 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8384 (mt0) cc_final: 0.8140 (mt0) REVERT: A 57 ARG cc_start: 0.8358 (tpt170) cc_final: 0.7804 (mmp-170) REVERT: A 94 GLU cc_start: 0.8740 (tt0) cc_final: 0.7873 (tm-30) REVERT: A 177 ASP cc_start: 0.7818 (m-30) cc_final: 0.6876 (t0) REVERT: A 247 ASP cc_start: 0.8316 (m-30) cc_final: 0.7743 (m-30) REVERT: A 308 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7554 (tpp-160) REVERT: B 57 ARG cc_start: 0.8369 (tpt170) cc_final: 0.7800 (mmp-170) REVERT: B 94 GLU cc_start: 0.8769 (tt0) cc_final: 0.7900 (tm-30) REVERT: B 177 ASP cc_start: 0.7819 (m-30) cc_final: 0.6931 (t0) REVERT: B 247 ASP cc_start: 0.8320 (m-30) cc_final: 0.7754 (m-30) REVERT: F 123 MET cc_start: 0.8669 (tpp) cc_final: 0.8380 (tpp) REVERT: C 57 ARG cc_start: 0.8372 (tpt170) cc_final: 0.7815 (mmp-170) REVERT: C 94 GLU cc_start: 0.8771 (tt0) cc_final: 0.7905 (tm-30) REVERT: C 177 ASP cc_start: 0.7821 (m-30) cc_final: 0.6900 (t0) REVERT: C 247 ASP cc_start: 0.8324 (m-30) cc_final: 0.7742 (m-30) REVERT: C 308 ARG cc_start: 0.7755 (tpp-160) cc_final: 0.7527 (tpp-160) REVERT: D 57 ARG cc_start: 0.8356 (tpt170) cc_final: 0.7791 (mmp-170) REVERT: D 94 GLU cc_start: 0.8762 (tt0) cc_final: 0.7911 (tm-30) REVERT: D 177 ASP cc_start: 0.7821 (m-30) cc_final: 0.6894 (t0) REVERT: D 247 ASP cc_start: 0.8324 (m-30) cc_final: 0.7754 (m-30) REVERT: H 123 MET cc_start: 0.8642 (tpp) cc_final: 0.8379 (tpp) outliers start: 25 outliers final: 8 residues processed: 200 average time/residue: 0.2126 time to fit residues: 58.7427 Evaluate side-chains 178 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.154785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112545 restraints weight = 8750.201| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.71 r_work: 0.3166 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8572 Z= 0.217 Angle : 0.558 6.448 11584 Z= 0.251 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.030 1447 Dihedral : 10.123 127.337 1210 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.83 % Allowed : 18.30 % Favored : 78.87 % 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: -1.43 (0.26), residues: 1042 helix: 0.17 (0.24), residues: 532 sheet: -2.41 (0.34), residues: 156 loop : -1.81 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 304 HIS 0.002 0.000 HIS D 92 PHE 0.017 0.001 PHE C 188 TYR 0.010 0.001 TYR D 274 ARG 0.002 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8171 (mt0) cc_final: 0.7917 (mt0) REVERT: A 57 ARG cc_start: 0.8306 (tpt170) cc_final: 0.7644 (mmp-170) REVERT: A 94 GLU cc_start: 0.8675 (tt0) cc_final: 0.7743 (tm-30) REVERT: A 177 ASP cc_start: 0.7711 (m-30) cc_final: 0.6759 (t0) REVERT: A 247 ASP cc_start: 0.8310 (m-30) cc_final: 0.7700 (m-30) REVERT: A 261 LYS cc_start: 0.5222 (OUTLIER) cc_final: 0.5015 (mptt) REVERT: A 308 ARG cc_start: 0.7626 (tpp-160) cc_final: 0.7346 (tpp-160) REVERT: B 57 ARG cc_start: 0.8318 (tpt170) cc_final: 0.7645 (mmp-170) REVERT: B 94 GLU cc_start: 0.8679 (tt0) cc_final: 0.7750 (tm-30) REVERT: B 177 ASP cc_start: 0.7711 (m-30) cc_final: 0.6751 (t0) REVERT: B 245 GLN cc_start: 0.8222 (mm-40) cc_final: 0.8020 (mm-40) REVERT: B 247 ASP cc_start: 0.8321 (m-30) cc_final: 0.7699 (m-30) REVERT: C 57 ARG cc_start: 0.8306 (tpt170) cc_final: 0.7652 (mmp-170) REVERT: C 94 GLU cc_start: 0.8684 (tt0) cc_final: 0.7740 (tm-30) REVERT: C 177 ASP cc_start: 0.7729 (m-30) cc_final: 0.6767 (t0) REVERT: C 247 ASP cc_start: 0.8309 (m-30) cc_final: 0.7680 (m-30) REVERT: C 261 LYS cc_start: 0.5245 (OUTLIER) cc_final: 0.5042 (mptt) REVERT: C 308 ARG cc_start: 0.7575 (tpp-160) cc_final: 0.7286 (tpp-160) REVERT: D 57 ARG cc_start: 0.8303 (tpt170) cc_final: 0.7633 (mmp-170) REVERT: D 94 GLU cc_start: 0.8687 (tt0) cc_final: 0.7741 (tm-30) REVERT: D 177 ASP cc_start: 0.7720 (m-30) cc_final: 0.6778 (t0) REVERT: D 247 ASP cc_start: 0.8320 (m-30) cc_final: 0.7695 (m-30) REVERT: D 261 LYS cc_start: 0.5222 (OUTLIER) cc_final: 0.5016 (mptt) outliers start: 26 outliers final: 12 residues processed: 200 average time/residue: 0.2271 time to fit residues: 62.3974 Evaluate side-chains 187 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112351 restraints weight = 8691.582| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.75 r_work: 0.3187 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 8572 Z= 0.226 Angle : 0.562 6.145 11584 Z= 0.252 Chirality : 0.041 0.132 1373 Planarity : 0.003 0.030 1447 Dihedral : 9.473 126.456 1210 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.49 % Allowed : 18.52 % Favored : 78.00 % 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: -0.70 (0.27), residues: 1042 helix: 0.60 (0.24), residues: 504 sheet: -2.19 (0.36), residues: 156 loop : -0.98 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 304 HIS 0.001 0.000 HIS C 92 PHE 0.020 0.001 PHE A 188 TYR 0.031 0.001 TYR D 274 ARG 0.002 0.000 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8381 (mt0) cc_final: 0.8123 (mt0) REVERT: A 57 ARG cc_start: 0.8349 (tpt170) cc_final: 0.7776 (mmp-170) REVERT: A 94 GLU cc_start: 0.8726 (tt0) cc_final: 0.7846 (tm-30) REVERT: A 177 ASP cc_start: 0.7831 (m-30) cc_final: 0.6958 (t0) REVERT: A 247 ASP cc_start: 0.8354 (m-30) cc_final: 0.7797 (m-30) REVERT: A 252 MET cc_start: 0.8686 (mtp) cc_final: 0.8134 (mtp) REVERT: A 261 LYS cc_start: 0.5308 (OUTLIER) cc_final: 0.4833 (tptt) REVERT: A 308 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7542 (tpp-160) REVERT: E 123 MET cc_start: 0.8448 (tpp) cc_final: 0.7719 (mmm) REVERT: B 57 ARG cc_start: 0.8353 (tpt170) cc_final: 0.7782 (mmp-170) REVERT: B 94 GLU cc_start: 0.8728 (tt0) cc_final: 0.7852 (tm-30) REVERT: B 177 ASP cc_start: 0.7984 (m-30) cc_final: 0.7086 (t0) REVERT: B 247 ASP cc_start: 0.8347 (m-30) cc_final: 0.7798 (m-30) REVERT: C 57 ARG cc_start: 0.8314 (tpt170) cc_final: 0.7772 (mmp-170) REVERT: C 94 GLU cc_start: 0.8719 (tt0) cc_final: 0.7830 (tm-30) REVERT: C 177 ASP cc_start: 0.7824 (m-30) cc_final: 0.6989 (t0) REVERT: C 247 ASP cc_start: 0.8338 (m-30) cc_final: 0.7782 (m-30) REVERT: C 252 MET cc_start: 0.8695 (mtp) cc_final: 0.8144 (mtp) REVERT: C 261 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.4857 (tptt) REVERT: C 308 ARG cc_start: 0.7777 (tpp-160) cc_final: 0.7466 (tpp-160) REVERT: D 57 ARG cc_start: 0.8349 (tpt170) cc_final: 0.7771 (mmp-170) REVERT: D 94 GLU cc_start: 0.8728 (tt0) cc_final: 0.7843 (tm-30) REVERT: D 177 ASP cc_start: 0.7827 (m-30) cc_final: 0.6960 (t0) REVERT: D 247 ASP cc_start: 0.8341 (m-30) cc_final: 0.7786 (m-30) REVERT: D 252 MET cc_start: 0.8684 (mtp) cc_final: 0.8120 (mtp) REVERT: D 261 LYS cc_start: 0.5312 (OUTLIER) cc_final: 0.5102 (mptt) REVERT: D 274 TYR cc_start: 0.7921 (t80) cc_final: 0.7584 (t80) REVERT: H 123 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7726 (mmt) outliers start: 32 outliers final: 18 residues processed: 197 average time/residue: 0.2337 time to fit residues: 62.8571 Evaluate side-chains 194 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113156 restraints weight = 8595.225| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.75 r_work: 0.3196 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8572 Z= 0.213 Angle : 0.559 6.034 11584 Z= 0.251 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.031 1447 Dihedral : 9.268 129.153 1210 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.81 % Allowed : 18.95 % Favored : 77.23 % 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: -0.51 (0.27), residues: 1042 helix: 0.73 (0.24), residues: 504 sheet: -1.96 (0.37), residues: 156 loop : -0.92 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 304 HIS 0.001 0.000 HIS D 92 PHE 0.026 0.002 PHE B 188 TYR 0.018 0.001 TYR D 274 ARG 0.001 0.000 ARG G 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8375 (mt0) cc_final: 0.8122 (mt0) REVERT: A 57 ARG cc_start: 0.8340 (tpt170) cc_final: 0.7765 (mmp-170) REVERT: A 94 GLU cc_start: 0.8695 (tt0) cc_final: 0.7861 (tm-30) REVERT: A 177 ASP cc_start: 0.7916 (m-30) cc_final: 0.7032 (t0) REVERT: A 247 ASP cc_start: 0.8344 (m-30) cc_final: 0.7787 (m-30) REVERT: A 261 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.4805 (ttmt) REVERT: A 308 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.7556 (tpp-160) REVERT: E 123 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8078 (mmm) REVERT: B 57 ARG cc_start: 0.8369 (tpt170) cc_final: 0.7772 (mmp-170) REVERT: B 94 GLU cc_start: 0.8698 (tt0) cc_final: 0.7861 (tm-30) REVERT: B 177 ASP cc_start: 0.7918 (m-30) cc_final: 0.7044 (t0) REVERT: B 247 ASP cc_start: 0.8343 (m-30) cc_final: 0.7797 (m-30) REVERT: B 252 MET cc_start: 0.8684 (mtp) cc_final: 0.8131 (mtp) REVERT: F 123 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7961 (mmm) REVERT: C 57 ARG cc_start: 0.8324 (tpt170) cc_final: 0.7767 (mmp-170) REVERT: C 94 GLU cc_start: 0.8699 (tt0) cc_final: 0.7848 (tm-30) REVERT: C 177 ASP cc_start: 0.7919 (m-30) cc_final: 0.7042 (t0) REVERT: C 247 ASP cc_start: 0.8341 (m-30) cc_final: 0.7790 (m-30) REVERT: C 261 LYS cc_start: 0.5318 (OUTLIER) cc_final: 0.4853 (ttmt) REVERT: C 308 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7461 (tpp-160) REVERT: G 123 MET cc_start: 0.8299 (tpp) cc_final: 0.7934 (mmm) REVERT: D 57 ARG cc_start: 0.8351 (tpt170) cc_final: 0.7766 (mmp-170) REVERT: D 94 GLU cc_start: 0.8718 (tt0) cc_final: 0.7856 (tm-30) REVERT: D 177 ASP cc_start: 0.7924 (m-30) cc_final: 0.7031 (t0) REVERT: D 247 ASP cc_start: 0.8353 (m-30) cc_final: 0.7796 (m-30) REVERT: D 261 LYS cc_start: 0.5266 (OUTLIER) cc_final: 0.4821 (tptt) REVERT: H 123 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8087 (mmm) outliers start: 35 outliers final: 23 residues processed: 197 average time/residue: 0.2101 time to fit residues: 56.5093 Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.1980 chunk 82 optimal weight: 0.0870 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.155258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112599 restraints weight = 8665.720| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.70 r_work: 0.3192 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 8572 Z= 0.255 Angle : 0.575 6.196 11584 Z= 0.260 Chirality : 0.042 0.132 1373 Planarity : 0.003 0.030 1447 Dihedral : 9.191 130.053 1210 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.36 % Allowed : 18.41 % Favored : 77.23 % 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: -0.50 (0.27), residues: 1042 helix: 0.69 (0.24), residues: 504 sheet: -1.82 (0.39), residues: 156 loop : -0.91 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 264 HIS 0.002 0.000 HIS D 92 PHE 0.026 0.001 PHE A 188 TYR 0.015 0.001 TYR D 274 ARG 0.001 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8262 (mt0) cc_final: 0.8006 (mt0) REVERT: A 57 ARG cc_start: 0.8305 (tpt170) cc_final: 0.7679 (mmp-170) REVERT: A 94 GLU cc_start: 0.8629 (tt0) cc_final: 0.7774 (tm-30) REVERT: A 123 MET cc_start: 0.8330 (mmm) cc_final: 0.7892 (mmm) REVERT: A 177 ASP cc_start: 0.7865 (m-30) cc_final: 0.6958 (t0) REVERT: A 247 ASP cc_start: 0.8352 (m-30) cc_final: 0.7765 (m-30) REVERT: A 252 MET cc_start: 0.8667 (mtp) cc_final: 0.8100 (mtp) REVERT: A 261 LYS cc_start: 0.5190 (OUTLIER) cc_final: 0.4753 (ttmt) REVERT: A 308 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.7300 (tpp-160) REVERT: E 123 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: B 57 ARG cc_start: 0.8316 (tpt170) cc_final: 0.7667 (mmp-170) REVERT: B 94 GLU cc_start: 0.8626 (tt0) cc_final: 0.7770 (tm-30) REVERT: B 177 ASP cc_start: 0.7829 (m-30) cc_final: 0.6898 (t0) REVERT: B 247 ASP cc_start: 0.8368 (m-30) cc_final: 0.7998 (m-30) REVERT: F 123 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7966 (mmm) REVERT: C 57 ARG cc_start: 0.8294 (tpt170) cc_final: 0.7683 (mmp-170) REVERT: C 94 GLU cc_start: 0.8630 (tt0) cc_final: 0.7758 (tm-30) REVERT: C 123 MET cc_start: 0.8321 (mmm) cc_final: 0.7992 (tpp) REVERT: C 177 ASP cc_start: 0.7870 (m-30) cc_final: 0.6972 (t0) REVERT: C 247 ASP cc_start: 0.8356 (m-30) cc_final: 0.7779 (m-30) REVERT: C 252 MET cc_start: 0.8671 (mtp) cc_final: 0.8103 (mtp) REVERT: C 261 LYS cc_start: 0.5191 (OUTLIER) cc_final: 0.4774 (ttmt) REVERT: C 308 ARG cc_start: 0.7640 (tpp-160) cc_final: 0.7224 (tpp-160) REVERT: D 57 ARG cc_start: 0.8305 (tpt170) cc_final: 0.7686 (mmp-170) REVERT: D 94 GLU cc_start: 0.8641 (tt0) cc_final: 0.7769 (tm-30) REVERT: D 177 ASP cc_start: 0.7874 (m-30) cc_final: 0.6964 (t0) REVERT: D 247 ASP cc_start: 0.8362 (m-30) cc_final: 0.7782 (m-30) REVERT: D 252 MET cc_start: 0.8665 (mtp) cc_final: 0.8094 (mtp) REVERT: D 261 LYS cc_start: 0.5198 (OUTLIER) cc_final: 0.4774 (ttmt) outliers start: 40 outliers final: 27 residues processed: 196 average time/residue: 0.2394 time to fit residues: 64.5796 Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113577 restraints weight = 8779.490| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.78 r_work: 0.3203 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8572 Z= 0.202 Angle : 0.567 7.240 11584 Z= 0.254 Chirality : 0.041 0.129 1373 Planarity : 0.003 0.030 1447 Dihedral : 8.933 127.958 1210 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.92 % Allowed : 18.85 % Favored : 77.23 % 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: -0.27 (0.28), residues: 1042 helix: 0.91 (0.25), residues: 504 sheet: -1.72 (0.40), residues: 156 loop : -0.84 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 264 HIS 0.001 0.000 HIS D 92 PHE 0.023 0.001 PHE D 188 TYR 0.013 0.001 TYR D 274 ARG 0.001 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8141 (mt0) cc_final: 0.7873 (mt0) REVERT: A 57 ARG cc_start: 0.8276 (tpt170) cc_final: 0.7616 (mmp-170) REVERT: A 94 GLU cc_start: 0.8573 (tt0) cc_final: 0.7706 (tm-30) REVERT: A 177 ASP cc_start: 0.7820 (m-30) cc_final: 0.6902 (t0) REVERT: A 247 ASP cc_start: 0.8339 (m-30) cc_final: 0.7750 (m-30) REVERT: A 261 LYS cc_start: 0.5114 (OUTLIER) cc_final: 0.4759 (ttmt) REVERT: A 308 ARG cc_start: 0.7573 (tpp-160) cc_final: 0.7291 (tpp-160) REVERT: E 123 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7887 (mmm) REVERT: B 57 ARG cc_start: 0.8291 (tpt170) cc_final: 0.7602 (mmp-170) REVERT: B 94 GLU cc_start: 0.8555 (tt0) cc_final: 0.7723 (tm-30) REVERT: B 123 MET cc_start: 0.8139 (mmm) cc_final: 0.7796 (tpp) REVERT: B 177 ASP cc_start: 0.7822 (m-30) cc_final: 0.6899 (t0) REVERT: B 247 ASP cc_start: 0.8336 (m-30) cc_final: 0.7956 (m-30) REVERT: C 57 ARG cc_start: 0.8265 (tpt170) cc_final: 0.7625 (mmp-170) REVERT: C 94 GLU cc_start: 0.8574 (tt0) cc_final: 0.7717 (tm-30) REVERT: C 123 MET cc_start: 0.8201 (mmm) cc_final: 0.7971 (mmm) REVERT: C 177 ASP cc_start: 0.7823 (m-30) cc_final: 0.6910 (t0) REVERT: C 247 ASP cc_start: 0.8322 (m-30) cc_final: 0.7724 (m-30) REVERT: C 261 LYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4862 (ttmt) REVERT: C 308 ARG cc_start: 0.7482 (tpp-160) cc_final: 0.7106 (tpp-160) REVERT: D 57 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7623 (mmp-170) REVERT: D 94 GLU cc_start: 0.8600 (tt0) cc_final: 0.7716 (tm-30) REVERT: D 177 ASP cc_start: 0.7819 (m-30) cc_final: 0.6897 (t0) REVERT: D 247 ASP cc_start: 0.8326 (m-30) cc_final: 0.7721 (m-30) REVERT: D 261 LYS cc_start: 0.5110 (OUTLIER) cc_final: 0.4808 (ttmt) REVERT: H 123 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7978 (mmt) outliers start: 36 outliers final: 22 residues processed: 197 average time/residue: 0.2053 time to fit residues: 55.1427 Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.157426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114498 restraints weight = 8655.490| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.71 r_work: 0.3218 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8572 Z= 0.194 Angle : 0.564 7.413 11584 Z= 0.253 Chirality : 0.041 0.129 1373 Planarity : 0.003 0.031 1447 Dihedral : 8.654 125.116 1210 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.70 % Allowed : 19.06 % Favored : 77.23 % 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: -0.16 (0.28), residues: 1042 helix: 1.07 (0.25), residues: 500 sheet: -1.68 (0.40), residues: 156 loop : -0.88 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 264 HIS 0.001 0.000 HIS D 92 PHE 0.022 0.001 PHE D 188 TYR 0.013 0.001 TYR D 274 ARG 0.001 0.000 ARG G 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8285 (tpt170) cc_final: 0.7653 (mmp-170) REVERT: A 94 GLU cc_start: 0.8593 (tt0) cc_final: 0.7755 (tm-30) REVERT: A 177 ASP cc_start: 0.7864 (m-30) cc_final: 0.6960 (t0) REVERT: A 247 ASP cc_start: 0.8076 (m-30) cc_final: 0.7515 (m-30) REVERT: A 261 LYS cc_start: 0.5190 (OUTLIER) cc_final: 0.4881 (ttmt) REVERT: E 123 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7900 (mmm) REVERT: B 57 ARG cc_start: 0.8299 (tpt170) cc_final: 0.7655 (mmp-170) REVERT: B 94 GLU cc_start: 0.8577 (tt0) cc_final: 0.7740 (tm-30) REVERT: B 177 ASP cc_start: 0.7867 (m-30) cc_final: 0.6961 (t0) REVERT: B 247 ASP cc_start: 0.8334 (m-30) cc_final: 0.7968 (m-30) REVERT: C 57 ARG cc_start: 0.8267 (tpt170) cc_final: 0.7680 (mmp-170) REVERT: C 94 GLU cc_start: 0.8579 (tt0) cc_final: 0.7759 (tm-30) REVERT: C 123 MET cc_start: 0.8204 (mmm) cc_final: 0.7936 (mmm) REVERT: C 177 ASP cc_start: 0.7870 (m-30) cc_final: 0.6971 (t0) REVERT: C 261 LYS cc_start: 0.5232 (OUTLIER) cc_final: 0.4946 (ttmt) REVERT: C 308 ARG cc_start: 0.7535 (tpp-160) cc_final: 0.7166 (tpp-160) REVERT: D 57 ARG cc_start: 0.8283 (tpt170) cc_final: 0.7675 (mmp-170) REVERT: D 94 GLU cc_start: 0.8588 (tt0) cc_final: 0.7774 (tm-30) REVERT: D 177 ASP cc_start: 0.7870 (m-30) cc_final: 0.6964 (t0) REVERT: D 247 ASP cc_start: 0.8335 (m-30) cc_final: 0.7751 (m-30) REVERT: D 261 LYS cc_start: 0.5219 (OUTLIER) cc_final: 0.4963 (ttmt) REVERT: H 123 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7513 (mmt) outliers start: 34 outliers final: 26 residues processed: 203 average time/residue: 0.1984 time to fit residues: 55.2680 Evaluate side-chains 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114610 restraints weight = 8586.171| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.68 r_work: 0.3221 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8572 Z= 0.203 Angle : 0.568 7.683 11584 Z= 0.254 Chirality : 0.041 0.129 1373 Planarity : 0.003 0.031 1447 Dihedral : 8.432 122.331 1210 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.27 % Allowed : 19.72 % Favored : 77.02 % 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: -0.13 (0.28), residues: 1042 helix: 1.09 (0.24), residues: 500 sheet: -1.68 (0.40), residues: 156 loop : -0.84 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 304 HIS 0.001 0.000 HIS D 92 PHE 0.007 0.001 PHE D 188 TYR 0.013 0.001 TYR D 274 ARG 0.001 0.000 ARG G 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8240 (tpt170) cc_final: 0.7584 (mmp-170) REVERT: A 94 GLU cc_start: 0.8527 (tt0) cc_final: 0.7714 (tm-30) REVERT: A 123 MET cc_start: 0.8266 (tpp) cc_final: 0.7357 (mmm) REVERT: A 177 ASP cc_start: 0.7818 (m-30) cc_final: 0.6956 (t0) REVERT: A 261 LYS cc_start: 0.5261 (OUTLIER) cc_final: 0.5008 (ttmt) REVERT: E 123 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7826 (mmm) REVERT: B 57 ARG cc_start: 0.8258 (tpt170) cc_final: 0.7614 (mmp-170) REVERT: B 94 GLU cc_start: 0.8525 (tt0) cc_final: 0.7700 (tm-30) REVERT: B 123 MET cc_start: 0.8277 (tpp) cc_final: 0.7787 (mmm) REVERT: B 177 ASP cc_start: 0.7824 (m-30) cc_final: 0.6906 (t0) REVERT: F 123 MET cc_start: 0.8090 (tpp) cc_final: 0.7728 (mmm) REVERT: C 57 ARG cc_start: 0.8237 (tpt170) cc_final: 0.7619 (mmp-170) REVERT: C 94 GLU cc_start: 0.8528 (tt0) cc_final: 0.7699 (tm-30) REVERT: C 123 MET cc_start: 0.8286 (mmm) cc_final: 0.7982 (mmm) REVERT: C 177 ASP cc_start: 0.7820 (m-30) cc_final: 0.6921 (t0) REVERT: C 261 LYS cc_start: 0.5329 (OUTLIER) cc_final: 0.5120 (ttmt) REVERT: C 308 ARG cc_start: 0.7473 (tpp-160) cc_final: 0.7099 (tpp-160) REVERT: G 123 MET cc_start: 0.8090 (tpp) cc_final: 0.7755 (mmm) REVERT: D 57 ARG cc_start: 0.8213 (tpt170) cc_final: 0.7489 (mmp-170) REVERT: D 94 GLU cc_start: 0.8533 (tt0) cc_final: 0.7697 (tm-30) REVERT: D 177 ASP cc_start: 0.7825 (m-30) cc_final: 0.6913 (t0) REVERT: D 247 ASP cc_start: 0.8317 (m-30) cc_final: 0.7715 (m-30) REVERT: D 261 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.5078 (ttmt) REVERT: H 123 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7625 (mmm) outliers start: 30 outliers final: 21 residues processed: 197 average time/residue: 0.2093 time to fit residues: 56.5584 Evaluate side-chains 201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114934 restraints weight = 8703.809| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.73 r_work: 0.3225 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8572 Z= 0.189 Angle : 0.564 7.694 11584 Z= 0.252 Chirality : 0.041 0.128 1373 Planarity : 0.002 0.031 1447 Dihedral : 8.129 118.871 1210 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.16 % Allowed : 19.83 % Favored : 77.02 % 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: 0.03 (0.28), residues: 1042 helix: 1.14 (0.24), residues: 518 sheet: -1.64 (0.40), residues: 156 loop : -0.70 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 304 HIS 0.001 0.000 HIS D 92 PHE 0.006 0.001 PHE B 335 TYR 0.013 0.001 TYR A 274 ARG 0.001 0.000 ARG D 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4167.93 seconds wall clock time: 74 minutes 13.65 seconds (4453.65 seconds total)