Starting phenix.real_space_refine on Sat Jun 7 11:21:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wx3_32875/06_2025/7wx3_32875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wx3_32875/06_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_32875/06_2025/7wx3_32875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wx3_32875/06_2025/7wx3_32875.map" model { file = "/net/cci-nas-00/data/ceres_data/7wx3_32875/06_2025/7wx3_32875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wx3_32875/06_2025/7wx3_32875.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 68 5.16 5 C 5296 2.51 5 N 1429 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.92, per 1000 atoms: 0.70 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: 2.27 Conformation dependent library (CDL) restraints added in 930.1 milliseconds 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: 0.90 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: 2.05 Time building geometry restraints manager: 2.61 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: 16.120 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.320 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.150 ------------------------------------------------------------------------------- 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 8576 Z= 0.475 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 Details of bonding type rmsd hydrogen bonds : bond 0.16463 ( 361) hydrogen bonds : angle 5.46973 ( 1002) covalent geometry : bond 0.01101 ( 8572) covalent geometry : angle 0.91432 (11584) Misc. bond : bond 0.00013 ( 4) *********************** 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 : 0.945 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: 0.2020 time to fit residues: 57.2533 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 : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 170 GLN C 52 GLN C 170 GLN D 52 GLN D 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.154479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112125 restraints weight = 8639.151| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.70 r_work: 0.3165 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8576 Z= 0.146 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 Details of bonding type rmsd hydrogen bonds : bond 0.05025 ( 361) hydrogen bonds : angle 4.09012 ( 1002) covalent geometry : bond 0.00339 ( 8572) covalent geometry : angle 0.57500 (11584) Misc. bond : bond 0.00049 ( 4) *********************** 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 : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8212 (mt0) cc_final: 0.7925 (mt0) REVERT: A 57 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7668 (mmp-170) REVERT: A 94 GLU cc_start: 0.8677 (tt0) cc_final: 0.7804 (tm-30) REVERT: A 177 ASP cc_start: 0.7671 (m-30) cc_final: 0.6700 (t0) REVERT: A 247 ASP cc_start: 0.8277 (m-30) cc_final: 0.7659 (m-30) REVERT: A 308 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7277 (tpp-160) REVERT: B 52 GLN cc_start: 0.8203 (mt0) cc_final: 0.7930 (mt0) REVERT: B 57 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7665 (mmp-170) REVERT: B 94 GLU cc_start: 0.8686 (tt0) cc_final: 0.7806 (tm-30) REVERT: B 177 ASP cc_start: 0.7674 (m-30) cc_final: 0.6703 (t0) REVERT: B 247 ASP cc_start: 0.8286 (m-30) cc_final: 0.7672 (m-30) REVERT: B 308 ARG cc_start: 0.7539 (tpp-160) cc_final: 0.7233 (tpp-160) REVERT: C 57 ARG cc_start: 0.8293 (tpt170) cc_final: 0.7673 (mmp-170) REVERT: C 94 GLU cc_start: 0.8699 (tt0) cc_final: 0.7799 (tm-30) REVERT: C 177 ASP cc_start: 0.7673 (m-30) cc_final: 0.6714 (t0) REVERT: C 247 ASP cc_start: 0.8277 (m-30) cc_final: 0.7654 (m-30) REVERT: C 308 ARG cc_start: 0.7519 (tpp-160) cc_final: 0.7206 (tpp-160) REVERT: D 57 ARG cc_start: 0.8275 (tpt170) cc_final: 0.7643 (mmp-170) REVERT: D 94 GLU cc_start: 0.8667 (tt0) cc_final: 0.7766 (tm-30) REVERT: D 177 ASP cc_start: 0.7675 (m-30) cc_final: 0.6702 (t0) REVERT: D 247 ASP cc_start: 0.8277 (m-30) cc_final: 0.7654 (m-30) REVERT: D 308 ARG cc_start: 0.7540 (tpp-160) cc_final: 0.7260 (tpp-160) outliers start: 11 outliers final: 5 residues processed: 179 average time/residue: 0.2007 time to fit residues: 49.3604 Evaluate side-chains 167 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain D residue 198 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.154299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112041 restraints weight = 8741.584| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.69 r_work: 0.3191 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8576 Z= 0.147 Angle : 0.566 6.325 11584 Z= 0.254 Chirality : 0.041 0.131 1373 Planarity : 0.003 0.026 1447 Dihedral : 10.778 131.977 1210 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.05 % Allowed : 18.41 % 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: 531 sheet: -2.62 (0.34), residues: 156 loop : -2.03 (0.30), residues: 355 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 0.015 0.001 PHE A 188 TYR 0.007 0.001 TYR C 274 ARG 0.002 0.000 ARG F 124 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 361) hydrogen bonds : angle 3.89808 ( 1002) covalent geometry : bond 0.00344 ( 8572) covalent geometry : angle 0.56551 (11584) Misc. bond : bond 0.00012 ( 4) *********************** 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 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8235 (mt0) cc_final: 0.7984 (mt0) REVERT: A 57 ARG cc_start: 0.8314 (tpt170) cc_final: 0.7702 (mmp-170) REVERT: A 94 GLU cc_start: 0.8724 (tt0) cc_final: 0.7839 (tm-30) REVERT: A 177 ASP cc_start: 0.7723 (m-30) cc_final: 0.6761 (t0) REVERT: A 247 ASP cc_start: 0.8305 (m-30) cc_final: 0.7690 (m-30) REVERT: B 57 ARG cc_start: 0.8329 (tpt170) cc_final: 0.7697 (mmp-170) REVERT: B 94 GLU cc_start: 0.8717 (tt0) cc_final: 0.7828 (tm-30) REVERT: B 177 ASP cc_start: 0.7726 (m-30) cc_final: 0.6809 (t0) REVERT: B 247 ASP cc_start: 0.8305 (m-30) cc_final: 0.7699 (m-30) REVERT: B 308 ARG cc_start: 0.7636 (tpp-160) cc_final: 0.7392 (tpp-160) REVERT: F 123 MET cc_start: 0.8595 (tpp) cc_final: 0.8295 (tpp) REVERT: C 57 ARG cc_start: 0.8330 (tpt170) cc_final: 0.7706 (mmp-170) REVERT: C 94 GLU cc_start: 0.8725 (tt0) cc_final: 0.7832 (tm-30) REVERT: C 177 ASP cc_start: 0.7733 (m-30) cc_final: 0.6786 (t0) REVERT: C 247 ASP cc_start: 0.8310 (m-30) cc_final: 0.7703 (m-30) REVERT: C 308 ARG cc_start: 0.7611 (tpp-160) cc_final: 0.7370 (tpp-160) REVERT: D 57 ARG cc_start: 0.8318 (tpt170) cc_final: 0.7685 (mmp-170) REVERT: D 94 GLU cc_start: 0.8729 (tt0) cc_final: 0.7826 (tm-30) REVERT: D 177 ASP cc_start: 0.7732 (m-30) cc_final: 0.6778 (t0) REVERT: D 247 ASP cc_start: 0.8310 (m-30) cc_final: 0.7702 (m-30) REVERT: D 308 ARG cc_start: 0.7671 (tpp-160) cc_final: 0.7469 (tpp-160) REVERT: H 123 MET cc_start: 0.8587 (tpp) cc_final: 0.8320 (tpp) outliers start: 28 outliers final: 10 residues processed: 199 average time/residue: 0.2841 time to fit residues: 77.7848 Evaluate side-chains 180 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 D residue 276 SER Chi-restraints excluded: chain D residue 310 VAL 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: 0.3980 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.157614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115166 restraints weight = 8697.667| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.73 r_work: 0.3231 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8576 Z= 0.106 Angle : 0.540 6.421 11584 Z= 0.241 Chirality : 0.040 0.127 1373 Planarity : 0.002 0.031 1447 Dihedral : 9.997 126.702 1210 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.51 % Allowed : 18.52 % Favored : 78.98 % 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: -0.76 (0.27), residues: 1042 helix: 0.63 (0.25), residues: 504 sheet: -2.37 (0.33), residues: 156 loop : -1.07 (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 0.014 0.001 PHE C 188 TYR 0.011 0.001 TYR D 274 ARG 0.002 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 361) hydrogen bonds : angle 3.64114 ( 1002) covalent geometry : bond 0.00235 ( 8572) covalent geometry : angle 0.53990 (11584) Misc. bond : bond 0.00007 ( 4) *********************** 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 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 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: 0.8155 (mt0) cc_final: 0.7896 (mt0) REVERT: A 57 ARG cc_start: 0.8297 (tpt170) cc_final: 0.7643 (mmp-170) REVERT: A 94 GLU cc_start: 0.8690 (tt0) cc_final: 0.7708 (tm-30) REVERT: A 177 ASP cc_start: 0.7696 (m-30) cc_final: 0.6743 (t0) REVERT: A 247 ASP cc_start: 0.8284 (m-30) cc_final: 0.7638 (m-30) REVERT: E 123 MET cc_start: 0.8199 (tpp) cc_final: 0.7864 (mmm) REVERT: B 52 GLN cc_start: 0.8152 (mt0) cc_final: 0.7895 (mt0) REVERT: B 57 ARG cc_start: 0.8310 (tpt170) cc_final: 0.7633 (mmp-170) REVERT: B 94 GLU cc_start: 0.8693 (tt0) cc_final: 0.7706 (tm-30) REVERT: B 177 ASP cc_start: 0.7701 (m-30) cc_final: 0.6787 (t0) REVERT: B 245 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7939 (mm-40) REVERT: B 247 ASP cc_start: 0.8297 (m-30) cc_final: 0.7657 (m-30) REVERT: C 57 ARG cc_start: 0.8313 (tpt170) cc_final: 0.7651 (mmp-170) REVERT: C 94 GLU cc_start: 0.8748 (tt0) cc_final: 0.7765 (tm-30) REVERT: C 177 ASP cc_start: 0.7715 (m-30) cc_final: 0.6772 (t0) REVERT: C 247 ASP cc_start: 0.8285 (m-30) cc_final: 0.7641 (m-30) REVERT: D 57 ARG cc_start: 0.8306 (tpt170) cc_final: 0.7621 (mmp-170) REVERT: D 94 GLU cc_start: 0.8735 (tt0) cc_final: 0.7744 (tm-30) REVERT: D 177 ASP cc_start: 0.7706 (m-30) cc_final: 0.6742 (t0) REVERT: D 245 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7929 (mm-40) REVERT: D 247 ASP cc_start: 0.8292 (m-30) cc_final: 0.7651 (m-30) outliers start: 23 outliers final: 11 residues processed: 190 average time/residue: 0.2051 time to fit residues: 53.1866 Evaluate side-chains 180 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain B residue 160 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 C residue 198 ASN Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 198 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112590 restraints weight = 8671.652| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.75 r_work: 0.3167 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8576 Z= 0.150 Angle : 0.560 6.233 11584 Z= 0.251 Chirality : 0.041 0.129 1373 Planarity : 0.002 0.028 1447 Dihedral : 9.486 125.935 1210 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.61 % Allowed : 19.06 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.27), residues: 1042 helix: 0.65 (0.24), residues: 504 sheet: -2.16 (0.35), residues: 156 loop : -1.00 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 304 HIS 0.002 0.001 HIS D 92 PHE 0.025 0.001 PHE A 188 TYR 0.007 0.001 TYR B 274 ARG 0.002 0.000 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 361) hydrogen bonds : angle 3.73144 ( 1002) covalent geometry : bond 0.00353 ( 8572) covalent geometry : angle 0.56001 (11584) Misc. bond : bond 0.00013 ( 4) *********************** 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 198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8101 (mt0) cc_final: 0.7833 (mt0) REVERT: A 57 ARG cc_start: 0.8281 (tpt170) cc_final: 0.7597 (mmp-170) REVERT: A 94 GLU cc_start: 0.8642 (tt0) cc_final: 0.7675 (tm-30) REVERT: A 177 ASP cc_start: 0.7757 (m-30) cc_final: 0.6829 (t0) REVERT: A 247 ASP cc_start: 0.8306 (m-30) cc_final: 0.7671 (m-30) REVERT: B 57 ARG cc_start: 0.8288 (tpt170) cc_final: 0.7602 (mmp-170) REVERT: B 94 GLU cc_start: 0.8645 (tt0) cc_final: 0.7678 (tm-30) REVERT: B 177 ASP cc_start: 0.7858 (m-30) cc_final: 0.6930 (t0) REVERT: B 247 ASP cc_start: 0.8306 (m-30) cc_final: 0.7661 (m-30) REVERT: C 57 ARG cc_start: 0.8276 (tpt170) cc_final: 0.7607 (mmp-170) REVERT: C 94 GLU cc_start: 0.8647 (tt0) cc_final: 0.7661 (tm-30) REVERT: C 177 ASP cc_start: 0.7768 (m-30) cc_final: 0.6865 (t0) REVERT: C 247 ASP cc_start: 0.8298 (m-30) cc_final: 0.7665 (m-30) REVERT: D 57 ARG cc_start: 0.8275 (tpt170) cc_final: 0.7589 (mmp-170) REVERT: D 94 GLU cc_start: 0.8651 (tt0) cc_final: 0.7669 (tm-30) REVERT: D 177 ASP cc_start: 0.7766 (m-30) cc_final: 0.6841 (t0) REVERT: D 247 ASP cc_start: 0.8303 (m-30) cc_final: 0.7657 (m-30) REVERT: H 123 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7608 (mmt) outliers start: 24 outliers final: 14 residues processed: 189 average time/residue: 0.1952 time to fit residues: 51.0121 Evaluate side-chains 187 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 296 ASP 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 123 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain C residue 198 ASN 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 198 ASN Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 47 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.157341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114601 restraints weight = 8553.247| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.74 r_work: 0.3190 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8576 Z= 0.125 Angle : 0.546 6.043 11584 Z= 0.245 Chirality : 0.040 0.128 1373 Planarity : 0.002 0.027 1447 Dihedral : 9.141 127.803 1210 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.72 % Allowed : 20.04 % 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: -0.36 (0.27), residues: 1042 helix: 0.87 (0.25), residues: 504 sheet: -1.90 (0.37), residues: 156 loop : -0.88 (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 0.009 0.001 PHE D 336 TYR 0.016 0.001 TYR D 274 ARG 0.001 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 361) hydrogen bonds : angle 3.64420 ( 1002) covalent geometry : bond 0.00286 ( 8572) covalent geometry : angle 0.54593 (11584) Misc. bond : bond 0.00010 ( 4) *********************** 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 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.849 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: 0.7579 (mmp-170) REVERT: A 94 GLU cc_start: 0.8619 (tt0) cc_final: 0.7662 (tm-30) REVERT: A 177 ASP cc_start: 0.7854 (m-30) cc_final: 0.6913 (t0) REVERT: A 247 ASP cc_start: 0.8315 (m-30) cc_final: 0.7698 (m-30) REVERT: B 57 ARG cc_start: 0.8287 (tpt170) cc_final: 0.7599 (mmp-170) REVERT: B 94 GLU cc_start: 0.8637 (tt0) cc_final: 0.7662 (tm-30) REVERT: B 177 ASP cc_start: 0.7841 (m-30) cc_final: 0.6901 (t0) REVERT: B 247 ASP cc_start: 0.8295 (m-30) cc_final: 0.7655 (m-30) REVERT: F 123 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7941 (mmt) REVERT: C 57 ARG cc_start: 0.8250 (tpt170) cc_final: 0.7584 (mmp-170) REVERT: C 94 GLU cc_start: 0.8624 (tt0) cc_final: 0.7647 (tm-30) REVERT: C 177 ASP cc_start: 0.7862 (m-30) cc_final: 0.6950 (t0) REVERT: C 247 ASP cc_start: 0.8320 (m-30) cc_final: 0.7695 (m-30) REVERT: D 57 ARG cc_start: 0.8273 (tpt170) cc_final: 0.7589 (mmp-170) REVERT: D 94 GLU cc_start: 0.8622 (tt0) cc_final: 0.7681 (tm-30) REVERT: D 177 ASP cc_start: 0.7866 (m-30) cc_final: 0.6916 (t0) REVERT: D 247 ASP cc_start: 0.8288 (m-30) cc_final: 0.7641 (m-30) REVERT: D 274 TYR cc_start: 0.7734 (t80) cc_final: 0.7498 (t80) REVERT: H 123 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7336 (mmt) outliers start: 25 outliers final: 18 residues processed: 187 average time/residue: 0.2036 time to fit residues: 52.3139 Evaluate side-chains 191 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 310 VAL 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 F residue 123 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET 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: 0.7980 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 99 optimal weight: 0.0470 chunk 84 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.157515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114402 restraints weight = 8616.358| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.77 r_work: 0.3190 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8576 Z= 0.127 Angle : 0.548 5.947 11584 Z= 0.245 Chirality : 0.040 0.127 1373 Planarity : 0.002 0.027 1447 Dihedral : 8.902 128.239 1210 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.38 % Allowed : 19.50 % 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: -0.20 (0.28), residues: 1042 helix: 0.98 (0.25), residues: 504 sheet: -1.75 (0.39), residues: 156 loop : -0.80 (0.34), residues: 382 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 0.022 0.001 PHE B 188 TYR 0.013 0.001 TYR D 274 ARG 0.001 0.000 ARG E 124 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 361) hydrogen bonds : angle 3.61519 ( 1002) covalent geometry : bond 0.00294 ( 8572) covalent geometry : angle 0.54795 (11584) Misc. bond : bond 0.00010 ( 4) *********************** 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 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8286 (tpt170) cc_final: 0.7633 (mmp-170) REVERT: A 94 GLU cc_start: 0.8601 (tt0) cc_final: 0.7704 (tm-30) REVERT: A 123 MET cc_start: 0.8175 (mmm) cc_final: 0.7645 (tpp) REVERT: A 177 ASP cc_start: 0.7879 (m-30) cc_final: 0.6931 (t0) REVERT: A 247 ASP cc_start: 0.8330 (m-30) cc_final: 0.7728 (m-30) REVERT: B 57 ARG cc_start: 0.8318 (tpt170) cc_final: 0.7652 (mmp-170) REVERT: B 94 GLU cc_start: 0.8629 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 123 MET cc_start: 0.8134 (mmm) cc_final: 0.7421 (tpp) REVERT: B 177 ASP cc_start: 0.7888 (m-30) cc_final: 0.6930 (t0) REVERT: B 247 ASP cc_start: 0.8343 (m-30) cc_final: 0.7727 (m-30) REVERT: C 57 ARG cc_start: 0.8276 (tpt170) cc_final: 0.7634 (mmp-170) REVERT: C 94 GLU cc_start: 0.8613 (tt0) cc_final: 0.7698 (tm-30) REVERT: C 177 ASP cc_start: 0.7911 (m-30) cc_final: 0.6990 (t0) REVERT: C 247 ASP cc_start: 0.8329 (m-30) cc_final: 0.7722 (m-30) REVERT: D 57 ARG cc_start: 0.8289 (tpt170) cc_final: 0.7630 (mmp-170) REVERT: D 94 GLU cc_start: 0.8619 (tt0) cc_final: 0.7711 (tm-30) REVERT: D 123 MET cc_start: 0.8371 (mmm) cc_final: 0.7929 (tpp) REVERT: D 177 ASP cc_start: 0.7890 (m-30) cc_final: 0.6928 (t0) REVERT: D 247 ASP cc_start: 0.8339 (m-30) cc_final: 0.7738 (m-30) REVERT: H 123 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7888 (mmt) outliers start: 31 outliers final: 17 residues processed: 188 average time/residue: 0.1998 time to fit residues: 51.6201 Evaluate side-chains 188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN 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 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 276 SER 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 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 127 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 0.0070 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.157967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114859 restraints weight = 8718.331| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.79 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: 0.7307 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8576 Z= 0.122 Angle : 0.553 5.952 11584 Z= 0.248 Chirality : 0.040 0.127 1373 Planarity : 0.002 0.026 1447 Dihedral : 8.674 127.193 1210 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.38 % Allowed : 19.06 % 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: -0.08 (0.28), residues: 1042 helix: 1.11 (0.25), residues: 503 sheet: -1.68 (0.39), residues: 156 loop : -0.78 (0.34), residues: 383 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 0.021 0.001 PHE D 188 TYR 0.012 0.001 TYR A 274 ARG 0.001 0.000 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 361) hydrogen bonds : angle 3.57373 ( 1002) covalent geometry : bond 0.00279 ( 8572) covalent geometry : angle 0.55308 (11584) Misc. bond : bond 0.00010 ( 4) *********************** 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 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8271 (tpt170) cc_final: 0.7574 (mmp-170) REVERT: A 94 GLU cc_start: 0.8578 (tt0) cc_final: 0.7649 (tm-30) REVERT: A 123 MET cc_start: 0.8158 (mmm) cc_final: 0.7430 (tpp) REVERT: A 177 ASP cc_start: 0.7835 (m-30) cc_final: 0.6884 (t0) REVERT: A 193 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 247 ASP cc_start: 0.8058 (m-30) cc_final: 0.7471 (m-30) REVERT: B 57 ARG cc_start: 0.8297 (tpt170) cc_final: 0.7600 (mmp-170) REVERT: B 94 GLU cc_start: 0.8590 (tt0) cc_final: 0.7651 (tm-30) REVERT: B 123 MET cc_start: 0.8156 (mmm) cc_final: 0.7465 (tpp) REVERT: B 177 ASP cc_start: 0.7849 (m-30) cc_final: 0.6886 (t0) REVERT: B 247 ASP cc_start: 0.8331 (m-30) cc_final: 0.7704 (m-30) REVERT: F 123 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7902 (mmt) REVERT: C 57 ARG cc_start: 0.8255 (tpt170) cc_final: 0.7588 (mmp-170) REVERT: C 94 GLU cc_start: 0.8591 (tt0) cc_final: 0.7639 (tm-30) REVERT: C 177 ASP cc_start: 0.7877 (m-30) cc_final: 0.6950 (t0) REVERT: C 247 ASP cc_start: 0.8313 (m-30) cc_final: 0.7699 (m-30) REVERT: D 57 ARG cc_start: 0.8269 (tpt170) cc_final: 0.7581 (mmp-170) REVERT: D 94 GLU cc_start: 0.8597 (tt0) cc_final: 0.7649 (tm-30) REVERT: D 123 MET cc_start: 0.8189 (mmm) cc_final: 0.7761 (tpp) REVERT: D 177 ASP cc_start: 0.7856 (m-30) cc_final: 0.6892 (t0) REVERT: D 247 ASP cc_start: 0.8325 (m-30) cc_final: 0.7718 (m-30) REVERT: H 123 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7697 (mmt) outliers start: 31 outliers final: 20 residues processed: 193 average time/residue: 0.2023 time to fit residues: 53.7781 Evaluate side-chains 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 261 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 21 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.156855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113550 restraints weight = 8644.097| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.78 r_work: 0.3172 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8576 Z= 0.150 Angle : 0.570 6.194 11584 Z= 0.256 Chirality : 0.041 0.129 1373 Planarity : 0.002 0.026 1447 Dihedral : 8.605 126.032 1210 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: -0.13 (0.28), residues: 1042 helix: 1.04 (0.24), residues: 503 sheet: -1.65 (0.40), residues: 156 loop : -0.79 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 304 HIS 0.002 0.000 HIS D 92 PHE 0.025 0.001 PHE C 188 TYR 0.012 0.001 TYR A 274 ARG 0.001 0.000 ARG H 124 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 361) hydrogen bonds : angle 3.65396 ( 1002) covalent geometry : bond 0.00354 ( 8572) covalent geometry : angle 0.56952 (11584) Misc. bond : bond 0.00011 ( 4) *********************** 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 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8281 (tpt170) cc_final: 0.7603 (mmp-170) REVERT: A 94 GLU cc_start: 0.8578 (tt0) cc_final: 0.7717 (tm-30) REVERT: A 123 MET cc_start: 0.8187 (mmm) cc_final: 0.7408 (tpp) REVERT: A 177 ASP cc_start: 0.7827 (m-30) cc_final: 0.6929 (t0) REVERT: A 247 ASP cc_start: 0.8087 (m-30) cc_final: 0.7512 (m-30) REVERT: B 57 ARG cc_start: 0.8294 (tpt170) cc_final: 0.7636 (mmp-170) REVERT: B 94 GLU cc_start: 0.8588 (tt0) cc_final: 0.7725 (tm-30) REVERT: B 123 MET cc_start: 0.8097 (mmm) cc_final: 0.7500 (tpp) REVERT: B 177 ASP cc_start: 0.7850 (m-30) cc_final: 0.6950 (t0) REVERT: F 123 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7746 (mmt) REVERT: C 57 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7644 (mmp-170) REVERT: C 94 GLU cc_start: 0.8596 (tt0) cc_final: 0.7743 (tm-30) REVERT: C 123 MET cc_start: 0.8060 (mmm) cc_final: 0.7735 (mtp) REVERT: C 177 ASP cc_start: 0.7921 (m-30) cc_final: 0.6966 (t0) REVERT: D 57 ARG cc_start: 0.8285 (tpt170) cc_final: 0.7634 (mmp-170) REVERT: D 94 GLU cc_start: 0.8604 (tt0) cc_final: 0.7746 (tm-30) REVERT: D 123 MET cc_start: 0.8211 (mmm) cc_final: 0.7653 (mmm) REVERT: D 177 ASP cc_start: 0.7842 (m-30) cc_final: 0.6934 (t0) REVERT: D 247 ASP cc_start: 0.8349 (m-30) cc_final: 0.7777 (m-30) REVERT: D 308 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7010 (tpp-160) REVERT: H 123 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7790 (mmt) outliers start: 28 outliers final: 24 residues processed: 194 average time/residue: 0.1962 time to fit residues: 52.3906 Evaluate side-chains 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU 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 126 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.157754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115146 restraints weight = 8557.406| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.68 r_work: 0.3224 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8576 Z= 0.133 Angle : 0.565 6.927 11584 Z= 0.253 Chirality : 0.041 0.127 1373 Planarity : 0.002 0.026 1447 Dihedral : 8.354 123.540 1210 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.61 % Allowed : 20.04 % 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: -0.01 (0.28), residues: 1042 helix: 1.17 (0.25), residues: 500 sheet: -1.59 (0.40), residues: 156 loop : -0.77 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 304 HIS 0.001 0.000 HIS D 92 PHE 0.023 0.001 PHE C 188 TYR 0.013 0.001 TYR A 274 ARG 0.001 0.000 ARG E 124 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 361) hydrogen bonds : angle 3.59077 ( 1002) covalent geometry : bond 0.00311 ( 8572) covalent geometry : angle 0.56476 (11584) Misc. bond : bond 0.00013 ( 4) ********************** 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 204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8240 (tpt170) cc_final: 0.7610 (mmp-170) REVERT: A 94 GLU cc_start: 0.8579 (tt0) cc_final: 0.7701 (tm-30) REVERT: A 177 ASP cc_start: 0.7835 (m-30) cc_final: 0.6951 (t0) REVERT: E 123 MET cc_start: 0.8129 (tpp) cc_final: 0.7373 (mmt) REVERT: B 57 ARG cc_start: 0.8263 (tpt170) cc_final: 0.7639 (mmp-170) REVERT: B 94 GLU cc_start: 0.8576 (tt0) cc_final: 0.7710 (tm-30) REVERT: B 123 MET cc_start: 0.8118 (mmm) cc_final: 0.7790 (tpp) REVERT: B 177 ASP cc_start: 0.7941 (m-30) cc_final: 0.6986 (t0) REVERT: F 123 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7156 (mmt) REVERT: C 57 ARG cc_start: 0.8242 (tpt170) cc_final: 0.7648 (mmp-170) REVERT: C 94 GLU cc_start: 0.8583 (tt0) cc_final: 0.7700 (tm-30) REVERT: C 177 ASP cc_start: 0.7922 (m-30) cc_final: 0.6985 (t0) REVERT: G 123 MET cc_start: 0.8205 (tpp) cc_final: 0.7731 (mmm) REVERT: D 57 ARG cc_start: 0.8222 (tpt170) cc_final: 0.7520 (mmp-170) REVERT: D 94 GLU cc_start: 0.8570 (tt0) cc_final: 0.7713 (tm-30) REVERT: D 177 ASP cc_start: 0.7948 (m-30) cc_final: 0.6993 (t0) REVERT: H 123 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7729 (mmt) outliers start: 24 outliers final: 18 residues processed: 197 average time/residue: 0.1979 time to fit residues: 53.7129 Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU 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 B residue 296 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 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 127 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET 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 59 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.154633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111931 restraints weight = 8731.091| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.70 r_work: 0.3182 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 8576 Z= 0.204 Angle : 0.612 7.361 11584 Z= 0.278 Chirality : 0.043 0.133 1373 Planarity : 0.003 0.025 1447 Dihedral : 8.563 122.774 1210 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.05 % Allowed : 19.61 % 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: -0.30 (0.27), residues: 1042 helix: 0.85 (0.24), residues: 500 sheet: -1.63 (0.41), residues: 156 loop : -0.84 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 304 HIS 0.002 0.001 HIS C 92 PHE 0.010 0.001 PHE B 335 TYR 0.013 0.001 TYR A 274 ARG 0.001 0.000 ARG F 124 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 361) hydrogen bonds : angle 3.79606 ( 1002) covalent geometry : bond 0.00495 ( 8572) covalent geometry : angle 0.61196 (11584) Misc. bond : bond 0.00017 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4034.82 seconds wall clock time: 70 minutes 50.89 seconds (4250.89 seconds total)