Starting phenix.real_space_refine on Thu Feb 13 04:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wx3_32875/02_2025/7wx3_32875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wx3_32875/02_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_32875/02_2025/7wx3_32875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wx3_32875/02_2025/7wx3_32875.map" model { file = "/net/cci-nas-00/data/ceres_data/7wx3_32875/02_2025/7wx3_32875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wx3_32875/02_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.52, per 1000 atoms: 0.65 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: 2.43 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: 0.93 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: 2.51 Time building geometry restraints manager: 2.71 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: 2.580 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: 0.090 Process input model: 22.400 Find NCS groups from input model: 0.430 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- 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 : 0.884 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: 0.1976 time to fit residues: 55.9662 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 : 0.887 ------------------------------------------------------------------------------- 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 = 0.112126 restraints weight = 8639.152| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.70 r_work: 0.3166 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.876 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: 0.8179 (mt0) cc_final: 0.7891 (mt0) REVERT: A 57 ARG cc_start: 0.8263 (tpt170) cc_final: 0.7644 (mmp-170) REVERT: A 94 GLU cc_start: 0.8667 (tt0) cc_final: 0.7785 (tm-30) REVERT: A 177 ASP cc_start: 0.7648 (m-30) cc_final: 0.6675 (t0) REVERT: A 247 ASP cc_start: 0.8270 (m-30) cc_final: 0.7645 (m-30) REVERT: A 308 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.7246 (tpp-160) REVERT: B 52 GLN cc_start: 0.8168 (mt0) cc_final: 0.7895 (mt0) REVERT: B 57 ARG cc_start: 0.8263 (tpt170) cc_final: 0.7641 (mmp-170) REVERT: B 94 GLU cc_start: 0.8675 (tt0) cc_final: 0.7788 (tm-30) REVERT: B 177 ASP cc_start: 0.7651 (m-30) cc_final: 0.6678 (t0) REVERT: B 247 ASP cc_start: 0.8279 (m-30) cc_final: 0.7657 (m-30) REVERT: B 308 ARG cc_start: 0.7509 (tpp-160) cc_final: 0.7201 (tpp-160) REVERT: C 57 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7649 (mmp-170) REVERT: C 94 GLU cc_start: 0.8689 (tt0) cc_final: 0.7781 (tm-30) REVERT: C 177 ASP cc_start: 0.7652 (m-30) cc_final: 0.6690 (t0) REVERT: C 247 ASP cc_start: 0.8271 (m-30) cc_final: 0.7641 (m-30) REVERT: C 308 ARG cc_start: 0.7487 (tpp-160) cc_final: 0.7174 (tpp-160) REVERT: D 57 ARG cc_start: 0.8260 (tpt170) cc_final: 0.7619 (mmp-170) REVERT: D 94 GLU cc_start: 0.8655 (tt0) cc_final: 0.7746 (tm-30) REVERT: D 177 ASP cc_start: 0.7653 (m-30) cc_final: 0.6677 (t0) REVERT: D 247 ASP cc_start: 0.8270 (m-30) cc_final: 0.7640 (m-30) REVERT: D 308 ARG cc_start: 0.7509 (tpp-160) cc_final: 0.7227 (tpp-160) outliers start: 11 outliers final: 5 residues processed: 179 average time/residue: 0.2138 time to fit residues: 52.2745 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 : 1.015 ------------------------------------------------------------------------------- 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: 0.9980 chunk 32 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.154522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111789 restraints weight = 8737.563| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.77 r_work: 0.3183 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1505 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= 0.218 Angle : 0.564 6.340 11584 Z= 0.254 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.026 1447 Dihedral : 10.722 132.008 1210 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.94 % Allowed : 18.52 % Favored : 78.54 % 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: -1.77 (0.26), residues: 1042 helix: -0.07 (0.24), residues: 532 sheet: -2.61 (0.34), residues: 156 loop : -2.03 (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 207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8392 (mt0) cc_final: 0.8147 (mt0) REVERT: A 57 ARG cc_start: 0.8365 (tpt170) cc_final: 0.7798 (mmp-170) REVERT: A 94 GLU cc_start: 0.8756 (tt0) cc_final: 0.7927 (tm-30) REVERT: A 177 ASP cc_start: 0.7822 (m-30) cc_final: 0.6884 (t0) REVERT: A 247 ASP cc_start: 0.8321 (m-30) cc_final: 0.7750 (m-30) REVERT: B 57 ARG cc_start: 0.8370 (tpt170) cc_final: 0.7802 (mmp-170) REVERT: B 94 GLU cc_start: 0.8746 (tt0) cc_final: 0.7911 (tm-30) REVERT: B 177 ASP cc_start: 0.7824 (m-30) cc_final: 0.6936 (t0) REVERT: B 247 ASP cc_start: 0.8322 (m-30) cc_final: 0.7755 (m-30) REVERT: B 308 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7532 (tpp-160) REVERT: F 123 MET cc_start: 0.8679 (tpp) cc_final: 0.8399 (tpp) REVERT: C 57 ARG cc_start: 0.8369 (tpt170) cc_final: 0.7813 (mmp-170) REVERT: C 94 GLU cc_start: 0.8754 (tt0) cc_final: 0.7918 (tm-30) REVERT: C 177 ASP cc_start: 0.7828 (m-30) cc_final: 0.6905 (t0) REVERT: C 247 ASP cc_start: 0.8326 (m-30) cc_final: 0.7758 (m-30) REVERT: C 308 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7541 (tpp-160) REVERT: D 57 ARG cc_start: 0.8361 (tpt170) cc_final: 0.7796 (mmp-170) REVERT: D 94 GLU cc_start: 0.8761 (tt0) cc_final: 0.7914 (tm-30) REVERT: D 177 ASP cc_start: 0.7826 (m-30) cc_final: 0.6898 (t0) REVERT: D 247 ASP cc_start: 0.8325 (m-30) cc_final: 0.7758 (m-30) REVERT: D 308 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7573 (tpp-160) REVERT: H 123 MET cc_start: 0.8672 (tpp) cc_final: 0.8402 (tpp) outliers start: 27 outliers final: 8 residues processed: 200 average time/residue: 0.2142 time to fit residues: 58.1113 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 : 0.963 ------------------------------------------------------------------------------- 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: 0.6980 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.154829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112615 restraints weight = 8739.241| |-----------------------------------------------------------------------------| r_work (start): 0.3360 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: 0.1752 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= 0.214 Angle : 0.558 6.428 11584 Z= 0.251 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.030 1447 Dihedral : 10.108 127.404 1210 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.94 % Allowed : 18.41 % Favored : 78.65 % 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: -1.44 (0.26), residues: 1042 helix: 0.15 (0.24), residues: 532 sheet: -2.42 (0.34), residues: 156 loop : -1.82 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 304 HIS 0.001 0.000 HIS D 92 PHE 0.017 0.001 PHE C 188 TYR 0.011 0.001 TYR D 274 ARG 0.002 0.000 ARG A 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 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8169 (mt0) cc_final: 0.7912 (mt0) REVERT: A 57 ARG cc_start: 0.8303 (tpt170) cc_final: 0.7643 (mmp-170) REVERT: A 94 GLU cc_start: 0.8673 (tt0) cc_final: 0.7743 (tm-30) REVERT: A 177 ASP cc_start: 0.7715 (m-30) cc_final: 0.6765 (t0) REVERT: A 247 ASP cc_start: 0.8310 (m-30) cc_final: 0.7700 (m-30) REVERT: A 261 LYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4927 (mptt) REVERT: B 57 ARG cc_start: 0.8313 (tpt170) cc_final: 0.7643 (mmp-170) REVERT: B 94 GLU cc_start: 0.8678 (tt0) cc_final: 0.7747 (tm-30) REVERT: B 177 ASP cc_start: 0.7710 (m-30) cc_final: 0.6750 (t0) REVERT: B 245 GLN cc_start: 0.8223 (mm-40) cc_final: 0.8020 (mm-40) REVERT: B 247 ASP cc_start: 0.8317 (m-30) cc_final: 0.7693 (m-30) REVERT: B 308 ARG cc_start: 0.7592 (tpp-160) cc_final: 0.7390 (tpp-160) REVERT: C 57 ARG cc_start: 0.8313 (tpt170) cc_final: 0.7652 (mmp-170) REVERT: C 94 GLU cc_start: 0.8680 (tt0) cc_final: 0.7736 (tm-30) REVERT: C 177 ASP cc_start: 0.7728 (m-30) cc_final: 0.6767 (t0) REVERT: C 247 ASP cc_start: 0.8307 (m-30) cc_final: 0.7677 (m-30) REVERT: C 261 LYS cc_start: 0.5252 (OUTLIER) cc_final: 0.5049 (mptt) REVERT: C 308 ARG cc_start: 0.7542 (tpp-160) cc_final: 0.7256 (tpp-160) REVERT: D 57 ARG cc_start: 0.8302 (tpt170) cc_final: 0.7633 (mmp-170) REVERT: D 94 GLU cc_start: 0.8684 (tt0) cc_final: 0.7739 (tm-30) REVERT: D 177 ASP cc_start: 0.7723 (m-30) cc_final: 0.6781 (t0) REVERT: D 247 ASP cc_start: 0.8316 (m-30) cc_final: 0.7691 (m-30) REVERT: D 261 LYS cc_start: 0.5145 (OUTLIER) cc_final: 0.4922 (mptt) outliers start: 27 outliers final: 13 residues processed: 200 average time/residue: 0.2162 time to fit residues: 58.8501 Evaluate side-chains 188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 12 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 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: 4.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.154065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111229 restraints weight = 8706.457| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.76 r_work: 0.3146 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1829 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= 0.262 Angle : 0.577 6.233 11584 Z= 0.260 Chirality : 0.042 0.131 1373 Planarity : 0.003 0.030 1447 Dihedral : 9.632 127.114 1210 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.70 % Allowed : 18.30 % 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: -1.32 (0.26), residues: 1042 helix: 0.21 (0.24), residues: 532 sheet: -2.21 (0.36), residues: 156 loop : -1.75 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 304 HIS 0.002 0.001 HIS D 92 PHE 0.023 0.001 PHE A 188 TYR 0.030 0.001 TYR D 274 ARG 0.002 0.000 ARG D 308 *********************** 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 211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8293 (tpt170) cc_final: 0.7611 (mmp-170) REVERT: A 94 GLU cc_start: 0.8637 (tt0) cc_final: 0.7696 (tm-30) REVERT: A 123 MET cc_start: 0.8404 (tpp) cc_final: 0.7515 (mmm) REVERT: A 177 ASP cc_start: 0.7609 (m-30) cc_final: 0.6693 (t0) REVERT: A 247 ASP cc_start: 0.8336 (m-30) cc_final: 0.7715 (m-30) REVERT: A 261 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4608 (ttmt) REVERT: B 57 ARG cc_start: 0.8297 (tpt170) cc_final: 0.7615 (mmp-170) REVERT: B 94 GLU cc_start: 0.8678 (tt0) cc_final: 0.7747 (tm-30) REVERT: B 177 ASP cc_start: 0.7692 (m-30) cc_final: 0.6788 (t0) REVERT: B 247 ASP cc_start: 0.8342 (m-30) cc_final: 0.7737 (m-30) REVERT: B 308 ARG cc_start: 0.7613 (tpp-160) cc_final: 0.7324 (tpp-160) REVERT: F 123 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7674 (mmt) REVERT: C 57 ARG cc_start: 0.8264 (tpt170) cc_final: 0.7608 (mmp-170) REVERT: C 94 GLU cc_start: 0.8672 (tt0) cc_final: 0.7730 (tm-30) REVERT: C 123 MET cc_start: 0.8389 (tpp) cc_final: 0.7480 (mmm) REVERT: C 177 ASP cc_start: 0.7605 (m-30) cc_final: 0.6705 (t0) REVERT: C 247 ASP cc_start: 0.8330 (m-30) cc_final: 0.7716 (m-30) REVERT: C 261 LYS cc_start: 0.5088 (OUTLIER) cc_final: 0.4671 (tptt) REVERT: C 308 ARG cc_start: 0.7604 (tpp-160) cc_final: 0.7226 (tpp-160) REVERT: D 57 ARG cc_start: 0.8287 (tpt170) cc_final: 0.7605 (mmp-170) REVERT: D 94 GLU cc_start: 0.8681 (tt0) cc_final: 0.7732 (tm-30) REVERT: D 177 ASP cc_start: 0.7610 (m-30) cc_final: 0.6687 (t0) REVERT: D 247 ASP cc_start: 0.8335 (m-30) cc_final: 0.7723 (m-30) REVERT: D 261 LYS cc_start: 0.5075 (OUTLIER) cc_final: 0.4628 (ttmt) REVERT: H 123 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7721 (mmt) outliers start: 34 outliers final: 22 residues processed: 201 average time/residue: 0.2075 time to fit residues: 57.1047 Evaluate side-chains 201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 240 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 117 LEU 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 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 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 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: 4.9990 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.155220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112448 restraints weight = 8612.957| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.74 r_work: 0.3162 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8572 Z= 0.232 Angle : 0.567 6.036 11584 Z= 0.256 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.031 1447 Dihedral : 9.395 130.007 1210 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.92 % Allowed : 18.74 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 1042 helix: 0.64 (0.24), residues: 504 sheet: -2.02 (0.37), residues: 156 loop : -1.00 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 304 HIS 0.001 0.000 HIS C 92 PHE 0.010 0.001 PHE A 188 TYR 0.017 0.001 TYR D 274 ARG 0.001 0.000 ARG E 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 208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8190 (mt0) cc_final: 0.7927 (mt0) REVERT: A 57 ARG cc_start: 0.8297 (tpt170) cc_final: 0.7633 (mmp-170) REVERT: A 94 GLU cc_start: 0.8651 (tt0) cc_final: 0.7722 (tm-30) REVERT: A 177 ASP cc_start: 0.7810 (m-30) cc_final: 0.6891 (t0) REVERT: A 247 ASP cc_start: 0.8330 (m-30) cc_final: 0.7723 (m-30) REVERT: A 252 MET cc_start: 0.8642 (mtp) cc_final: 0.8097 (mtp) REVERT: A 261 LYS cc_start: 0.5074 (OUTLIER) cc_final: 0.4598 (ttmt) REVERT: B 57 ARG cc_start: 0.8312 (tpt170) cc_final: 0.7640 (mmp-170) REVERT: B 94 GLU cc_start: 0.8658 (tt0) cc_final: 0.7729 (tm-30) REVERT: B 177 ASP cc_start: 0.7823 (m-30) cc_final: 0.6898 (t0) REVERT: B 247 ASP cc_start: 0.8341 (m-30) cc_final: 0.7743 (m-30) REVERT: B 252 MET cc_start: 0.8653 (mtp) cc_final: 0.8100 (mtp) REVERT: B 308 ARG cc_start: 0.7609 (tpp-160) cc_final: 0.7361 (tpp-160) REVERT: F 123 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7895 (mmm) REVERT: C 57 ARG cc_start: 0.8277 (tpt170) cc_final: 0.7635 (mmp-170) REVERT: C 94 GLU cc_start: 0.8621 (tt0) cc_final: 0.7725 (tm-30) REVERT: C 177 ASP cc_start: 0.7816 (m-30) cc_final: 0.6903 (t0) REVERT: C 247 ASP cc_start: 0.8326 (m-30) cc_final: 0.7727 (m-30) REVERT: C 252 MET cc_start: 0.8649 (mtp) cc_final: 0.8094 (mtp) REVERT: C 261 LYS cc_start: 0.5101 (OUTLIER) cc_final: 0.4699 (tptt) REVERT: C 308 ARG cc_start: 0.7601 (tpp-160) cc_final: 0.7270 (tpp-160) REVERT: D 57 ARG cc_start: 0.8295 (tpt170) cc_final: 0.7631 (mmp-170) REVERT: D 94 GLU cc_start: 0.8655 (tt0) cc_final: 0.7738 (tm-30) REVERT: D 177 ASP cc_start: 0.7817 (m-30) cc_final: 0.6888 (t0) REVERT: D 247 ASP cc_start: 0.8343 (m-30) cc_final: 0.7742 (m-30) REVERT: D 252 MET cc_start: 0.8647 (mtp) cc_final: 0.8088 (mtp) REVERT: D 261 LYS cc_start: 0.5075 (OUTLIER) cc_final: 0.4612 (ttmt) REVERT: H 123 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7879 (mmm) outliers start: 36 outliers final: 21 residues processed: 200 average time/residue: 0.2075 time to fit residues: 56.9016 Evaluate side-chains 197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 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 126 THR 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 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 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 276 SER 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: 0.5980 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.156645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113655 restraints weight = 8661.976| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.76 r_work: 0.3204 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8572 Z= 0.197 Angle : 0.558 6.220 11584 Z= 0.250 Chirality : 0.041 0.128 1373 Planarity : 0.003 0.031 1447 Dihedral : 9.121 130.087 1210 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.70 % Allowed : 19.17 % Favored : 77.12 % 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: -0.39 (0.27), residues: 1042 helix: 0.85 (0.25), residues: 504 sheet: -1.85 (0.38), residues: 156 loop : -0.92 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 264 HIS 0.001 0.000 HIS D 92 PHE 0.022 0.001 PHE B 188 TYR 0.014 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 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8394 (mt0) cc_final: 0.8145 (mt0) REVERT: A 57 ARG cc_start: 0.8359 (tpt170) cc_final: 0.7787 (mmp-170) REVERT: A 94 GLU cc_start: 0.8688 (tt0) cc_final: 0.7872 (tm-30) REVERT: A 177 ASP cc_start: 0.7937 (m-30) cc_final: 0.7061 (t0) REVERT: A 247 ASP cc_start: 0.8335 (m-30) cc_final: 0.7785 (m-30) REVERT: A 261 LYS cc_start: 0.5293 (OUTLIER) cc_final: 0.4844 (ttmt) REVERT: B 57 ARG cc_start: 0.8371 (tpt170) cc_final: 0.7788 (mmp-170) REVERT: B 94 GLU cc_start: 0.8696 (tt0) cc_final: 0.7877 (tm-30) REVERT: B 123 MET cc_start: 0.8398 (mmm) cc_final: 0.8024 (tpp) REVERT: B 177 ASP cc_start: 0.7931 (m-30) cc_final: 0.7063 (t0) REVERT: B 247 ASP cc_start: 0.8338 (m-30) cc_final: 0.7794 (m-30) REVERT: B 308 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.7477 (tpp-160) REVERT: F 123 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8165 (mmt) REVERT: C 57 ARG cc_start: 0.8336 (tpt170) cc_final: 0.7785 (mmp-170) REVERT: C 94 GLU cc_start: 0.8694 (tt0) cc_final: 0.7866 (tm-30) REVERT: C 177 ASP cc_start: 0.7938 (m-30) cc_final: 0.7065 (t0) REVERT: C 247 ASP cc_start: 0.8333 (m-30) cc_final: 0.7786 (m-30) REVERT: C 252 MET cc_start: 0.8684 (mtp) cc_final: 0.8175 (mtp) REVERT: C 261 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.4928 (ttmt) REVERT: C 308 ARG cc_start: 0.7740 (tpp-160) cc_final: 0.7477 (tpp-160) REVERT: D 57 ARG cc_start: 0.8354 (tpt170) cc_final: 0.7787 (mmp-170) REVERT: D 94 GLU cc_start: 0.8706 (tt0) cc_final: 0.7881 (tm-30) REVERT: D 123 MET cc_start: 0.8455 (mmm) cc_final: 0.8087 (tpp) REVERT: D 177 ASP cc_start: 0.7942 (m-30) cc_final: 0.7059 (t0) REVERT: D 247 ASP cc_start: 0.8345 (m-30) cc_final: 0.7796 (m-30) REVERT: D 261 LYS cc_start: 0.5291 (OUTLIER) cc_final: 0.4872 (ttmt) REVERT: H 123 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8149 (mmt) outliers start: 34 outliers final: 20 residues processed: 193 average time/residue: 0.2149 time to fit residues: 56.4894 Evaluate side-chains 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 119 MET 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 99 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.158191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115007 restraints weight = 8744.075| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.78 r_work: 0.3197 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8572 Z= 0.169 Angle : 0.551 6.587 11584 Z= 0.247 Chirality : 0.040 0.127 1373 Planarity : 0.003 0.031 1447 Dihedral : 8.800 127.620 1210 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.05 % Allowed : 19.50 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.28), residues: 1042 helix: 1.06 (0.25), residues: 504 sheet: -1.72 (0.39), residues: 156 loop : -0.83 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 264 HIS 0.001 0.000 HIS D 92 PHE 0.020 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 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8137 (mt0) cc_final: 0.7862 (mt0) REVERT: A 57 ARG cc_start: 0.8288 (tpt170) cc_final: 0.7620 (mmp-170) REVERT: A 94 GLU cc_start: 0.8604 (tt0) cc_final: 0.7695 (tm-30) REVERT: A 177 ASP cc_start: 0.7810 (m-30) cc_final: 0.6895 (t0) REVERT: A 247 ASP cc_start: 0.8323 (m-30) cc_final: 0.7715 (m-30) REVERT: A 261 LYS cc_start: 0.5135 (OUTLIER) cc_final: 0.4851 (ttmt) REVERT: B 57 ARG cc_start: 0.8295 (tpt170) cc_final: 0.7617 (mmp-170) REVERT: B 94 GLU cc_start: 0.8608 (tt0) cc_final: 0.7698 (tm-30) REVERT: B 123 MET cc_start: 0.8142 (mmm) cc_final: 0.7877 (tpp) REVERT: B 177 ASP cc_start: 0.7811 (m-30) cc_final: 0.6902 (t0) REVERT: B 247 ASP cc_start: 0.8318 (m-30) cc_final: 0.7718 (m-30) REVERT: B 308 ARG cc_start: 0.7456 (tpp-160) cc_final: 0.7243 (tpp-160) REVERT: F 123 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7911 (mmt) REVERT: C 57 ARG cc_start: 0.8272 (tpt170) cc_final: 0.7618 (mmp-170) REVERT: C 94 GLU cc_start: 0.8598 (tt0) cc_final: 0.7680 (tm-30) REVERT: C 177 ASP cc_start: 0.7888 (m-30) cc_final: 0.6929 (t0) REVERT: C 247 ASP cc_start: 0.8307 (m-30) cc_final: 0.7700 (m-30) REVERT: C 261 LYS cc_start: 0.5137 (OUTLIER) cc_final: 0.4883 (ttmt) REVERT: C 308 ARG cc_start: 0.7447 (tpp-160) cc_final: 0.7235 (tpp-160) REVERT: D 57 ARG cc_start: 0.8294 (tpt170) cc_final: 0.7618 (mmp-170) REVERT: D 94 GLU cc_start: 0.8621 (tt0) cc_final: 0.7698 (tm-30) REVERT: D 123 MET cc_start: 0.8220 (mmm) cc_final: 0.7891 (tpp) REVERT: D 177 ASP cc_start: 0.7817 (m-30) cc_final: 0.6905 (t0) REVERT: D 247 ASP cc_start: 0.8331 (m-30) cc_final: 0.7733 (m-30) REVERT: D 261 LYS cc_start: 0.5132 (OUTLIER) cc_final: 0.4823 (ttmt) REVERT: H 123 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7906 (mmt) outliers start: 28 outliers final: 13 residues processed: 192 average time/residue: 0.2138 time to fit residues: 55.9377 Evaluate side-chains 189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 126 THR Chi-restraints excluded: chain B residue 261 LYS 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 C residue 240 LEU 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 127 LEU Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 276 SER 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: 0.7980 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.156613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113334 restraints weight = 8667.131| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.77 r_work: 0.3172 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2204 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= 0.221 Angle : 0.569 6.520 11584 Z= 0.256 Chirality : 0.041 0.129 1373 Planarity : 0.003 0.031 1447 Dihedral : 8.708 125.775 1210 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.38 % Allowed : 19.39 % 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: 1.04 (0.25), residues: 503 sheet: -1.70 (0.40), residues: 156 loop : -0.84 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 304 HIS 0.001 0.000 HIS D 92 PHE 0.007 0.001 PHE D 188 TYR 0.012 0.001 TYR A 274 ARG 0.001 0.000 ARG H 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 207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8269 (tpt170) cc_final: 0.7570 (mmp-170) REVERT: A 94 GLU cc_start: 0.8560 (tt0) cc_final: 0.7673 (tm-30) REVERT: A 177 ASP cc_start: 0.7776 (m-30) cc_final: 0.6862 (t0) REVERT: A 247 ASP cc_start: 0.8073 (m-30) cc_final: 0.7488 (m-30) REVERT: A 261 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4925 (ttmt) REVERT: B 57 ARG cc_start: 0.8275 (tpt170) cc_final: 0.7570 (mmp-170) REVERT: B 94 GLU cc_start: 0.8573 (tt0) cc_final: 0.7677 (tm-30) REVERT: B 123 MET cc_start: 0.8226 (mmm) cc_final: 0.7800 (tpp) REVERT: B 177 ASP cc_start: 0.7788 (m-30) cc_final: 0.6860 (t0) REVERT: B 247 ASP cc_start: 0.8329 (m-30) cc_final: 0.7940 (m-30) REVERT: B 308 ARG cc_start: 0.7454 (tpp-160) cc_final: 0.7164 (tpp-160) REVERT: F 123 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7955 (mmt) REVERT: C 57 ARG cc_start: 0.8247 (tpt170) cc_final: 0.7562 (mmp-170) REVERT: C 94 GLU cc_start: 0.8537 (tt0) cc_final: 0.7674 (tm-30) REVERT: C 177 ASP cc_start: 0.7782 (m-30) cc_final: 0.6866 (t0) REVERT: C 261 LYS cc_start: 0.5140 (OUTLIER) cc_final: 0.4890 (ttmt) REVERT: D 57 ARG cc_start: 0.8264 (tpt170) cc_final: 0.7571 (mmp-170) REVERT: D 94 GLU cc_start: 0.8563 (tt0) cc_final: 0.7706 (tm-30) REVERT: D 123 MET cc_start: 0.8245 (mmm) cc_final: 0.7853 (tpp) REVERT: D 177 ASP cc_start: 0.7780 (m-30) cc_final: 0.6854 (t0) REVERT: D 247 ASP cc_start: 0.8346 (m-30) cc_final: 0.7963 (m-30) REVERT: D 261 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4875 (ttmt) outliers start: 31 outliers final: 22 residues processed: 197 average time/residue: 0.2129 time to fit residues: 57.3837 Evaluate side-chains 202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS 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 126 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 198 ASN 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 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 C residue 99 MET 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 276 SER 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 D residue 261 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 310 VAL 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: 1.9990 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.156842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114109 restraints weight = 8593.065| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.69 r_work: 0.3182 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2243 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= 0.214 Angle : 0.568 7.176 11584 Z= 0.255 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.031 1447 Dihedral : 8.520 123.153 1210 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.61 % Allowed : 19.83 % Favored : 77.56 % 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: -0.11 (0.28), residues: 1042 helix: 1.11 (0.25), residues: 500 sheet: -1.67 (0.40), residues: 156 loop : -0.85 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 304 HIS 0.001 0.000 HIS D 92 PHE 0.007 0.001 PHE D 335 TYR 0.013 0.001 TYR A 274 ARG 0.001 0.000 ARG H 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 197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8254 (tpt170) cc_final: 0.7586 (mmp-170) REVERT: A 94 GLU cc_start: 0.8546 (tt0) cc_final: 0.7706 (tm-30) REVERT: A 177 ASP cc_start: 0.7798 (m-30) cc_final: 0.6898 (t0) REVERT: A 261 LYS cc_start: 0.5140 (OUTLIER) cc_final: 0.4772 (ttmt) REVERT: B 57 ARG cc_start: 0.8273 (tpt170) cc_final: 0.7600 (mmp-170) REVERT: B 94 GLU cc_start: 0.8559 (tt0) cc_final: 0.7712 (tm-30) REVERT: B 123 MET cc_start: 0.8130 (mmm) cc_final: 0.7922 (tpp) REVERT: B 177 ASP cc_start: 0.7813 (m-30) cc_final: 0.6891 (t0) REVERT: B 247 ASP cc_start: 0.8318 (m-30) cc_final: 0.7936 (m-30) REVERT: B 308 ARG cc_start: 0.7488 (tpp-160) cc_final: 0.7107 (tpp-160) REVERT: F 123 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7759 (mmt) REVERT: C 57 ARG cc_start: 0.8256 (tpt170) cc_final: 0.7652 (mmp-170) REVERT: C 94 GLU cc_start: 0.8559 (tt0) cc_final: 0.7700 (tm-30) REVERT: C 177 ASP cc_start: 0.7800 (m-30) cc_final: 0.6958 (t0) REVERT: C 261 LYS cc_start: 0.5307 (OUTLIER) cc_final: 0.5063 (ttmt) REVERT: G 123 MET cc_start: 0.8086 (tpp) cc_final: 0.7846 (mmm) REVERT: D 57 ARG cc_start: 0.8247 (tpt170) cc_final: 0.7563 (mmp-170) REVERT: D 94 GLU cc_start: 0.8571 (tt0) cc_final: 0.7712 (tm-30) REVERT: D 177 ASP cc_start: 0.7805 (m-30) cc_final: 0.6900 (t0) REVERT: D 247 ASP cc_start: 0.8311 (m-30) cc_final: 0.7928 (m-30) REVERT: D 261 LYS cc_start: 0.5136 (OUTLIER) cc_final: 0.4778 (ttmt) outliers start: 24 outliers final: 18 residues processed: 192 average time/residue: 0.2175 time to fit residues: 56.8268 Evaluate side-chains 195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 198 ASN 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 296 ASP Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain C residue 99 MET 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 121 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 310 VAL 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: 0.8980 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 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 = 0.3887 r_free = 0.3887 target = 0.156617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113825 restraints weight = 8726.832| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.71 r_work: 0.3208 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2271 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= 0.222 Angle : 0.574 7.487 11584 Z= 0.258 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.031 1447 Dihedral : 8.357 120.607 1210 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.27 % Allowed : 19.17 % Favored : 77.56 % 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: -0.09 (0.28), residues: 1042 helix: 1.13 (0.25), residues: 500 sheet: -1.71 (0.40), residues: 156 loop : -0.81 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 304 HIS 0.001 0.000 HIS D 92 PHE 0.007 0.001 PHE B 335 TYR 0.013 0.001 TYR A 274 ARG 0.001 0.000 ARG G 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.50 seconds wall clock time: 66 minutes 50.14 seconds (4010.14 seconds total)