Starting phenix.real_space_refine on Wed Feb 4 23:41:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wjr_66027/02_2026/9wjr_66027.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wjr_66027/02_2026/9wjr_66027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wjr_66027/02_2026/9wjr_66027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wjr_66027/02_2026/9wjr_66027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wjr_66027/02_2026/9wjr_66027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wjr_66027/02_2026/9wjr_66027.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.088 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8952 2.51 5 N 2208 2.21 5 O 2388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13608 Number of models: 1 Model: "" Number of chains: 9 Chain: "Y" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1779 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "Z" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2745 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "F" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1779 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "G" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2745 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "S" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1779 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "T" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2745 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.09, per 1000 atoms: 0.23 Number of scatterers: 13608 At special positions: 0 Unit cell: (122.459, 131.052, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2388 8.00 N 2208 7.00 C 8952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 597.1 milliseconds 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 7 sheets defined 71.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'Y' and resid 2 through 23 removed outlier: 3.892A pdb=" N ILE Y 21 " --> pdb=" O GLY Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 41 removed outlier: 4.011A pdb=" N SER Y 35 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 59 removed outlier: 3.812A pdb=" N MET Y 56 " --> pdb=" O GLY Y 52 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE Y 57 " --> pdb=" O SER Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 71 through 86 removed outlier: 3.805A pdb=" N ALA Y 75 " --> pdb=" O ASP Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 97 removed outlier: 3.741A pdb=" N THR Y 95 " --> pdb=" O LEU Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 132 removed outlier: 4.507A pdb=" N VAL Y 121 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY Y 122 " --> pdb=" O PHE Y 118 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE Y 123 " --> pdb=" O LEU Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 164 removed outlier: 3.734A pdb=" N VAL Y 139 " --> pdb=" O SER Y 135 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE Y 154 " --> pdb=" O GLN Y 150 " (cutoff:3.500A) Proline residue: Y 157 - end of helix Processing helix chain 'Y' and resid 165 through 175 Processing helix chain 'Y' and resid 177 through 189 removed outlier: 3.672A pdb=" N GLY Y 189 " --> pdb=" O ALA Y 185 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 203 removed outlier: 4.020A pdb=" N GLY Y 195 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL Y 199 " --> pdb=" O GLY Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 219 Processing helix chain 'Y' and resid 225 through 246 Processing helix chain 'Z' and resid 11 through 23 Processing helix chain 'Z' and resid 36 through 51 removed outlier: 3.808A pdb=" N LEU Z 40 " --> pdb=" O ASN Z 36 " (cutoff:3.500A) Proline residue: Z 45 - end of helix Processing helix chain 'Z' and resid 55 through 65 removed outlier: 3.728A pdb=" N HIS Z 65 " --> pdb=" O ALA Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 91 Processing helix chain 'Z' and resid 97 through 121 removed outlier: 4.308A pdb=" N ILE Z 101 " --> pdb=" O ASP Z 97 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN Z 102 " --> pdb=" O GLU Z 98 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY Z 110 " --> pdb=" O VAL Z 106 " (cutoff:3.500A) Proline residue: Z 111 - end of helix Proline residue: Z 118 - end of helix Processing helix chain 'Z' and resid 123 through 137 Processing helix chain 'Z' and resid 141 through 170 Processing helix chain 'Z' and resid 173 through 178 Processing helix chain 'Z' and resid 180 through 205 removed outlier: 3.893A pdb=" N ILE Z 185 " --> pdb=" O MET Z 181 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL Z 205 " --> pdb=" O ILE Z 201 " (cutoff:3.500A) Processing helix chain 'Z' and resid 279 through 283 Processing helix chain 'Z' and resid 288 through 301 removed outlier: 4.128A pdb=" N HIS Z 292 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 312 through 320 Processing helix chain 'Z' and resid 322 through 340 removed outlier: 3.872A pdb=" N LYS Z 340 " --> pdb=" O LEU Z 336 " (cutoff:3.500A) Processing helix chain 'Z' and resid 343 through 363 Processing helix chain 'F' and resid 2 through 23 removed outlier: 3.918A pdb=" N ILE F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 removed outlier: 4.035A pdb=" N SER F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 59 removed outlier: 3.771A pdb=" N MET F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 86 removed outlier: 3.796A pdb=" N ALA F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 97 removed outlier: 3.772A pdb=" N THR F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 132 removed outlier: 4.485A pdb=" N VAL F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 164 removed outlier: 3.768A pdb=" N VAL F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE F 154 " --> pdb=" O GLN F 150 " (cutoff:3.500A) Proline residue: F 157 - end of helix Processing helix chain 'F' and resid 165 through 175 Processing helix chain 'F' and resid 177 through 189 removed outlier: 3.691A pdb=" N GLY F 189 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 removed outlier: 4.056A pdb=" N GLY F 195 " --> pdb=" O VAL F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 219 Processing helix chain 'F' and resid 225 through 247 removed outlier: 4.073A pdb=" N ALA F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 36 through 51 removed outlier: 3.863A pdb=" N LEU G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 55 through 65 removed outlier: 3.699A pdb=" N HIS G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 91 Processing helix chain 'G' and resid 98 through 121 removed outlier: 4.505A pdb=" N GLN G 102 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY G 110 " --> pdb=" O VAL G 106 " (cutoff:3.500A) Proline residue: G 111 - end of helix Proline residue: G 118 - end of helix Processing helix chain 'G' and resid 123 through 137 Processing helix chain 'G' and resid 141 through 170 Processing helix chain 'G' and resid 173 through 178 Processing helix chain 'G' and resid 180 through 205 removed outlier: 3.585A pdb=" N VAL G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 301 removed outlier: 4.099A pdb=" N HIS G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 320 Processing helix chain 'G' and resid 322 through 340 removed outlier: 3.981A pdb=" N LYS G 340 " --> pdb=" O LEU G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 362 Processing helix chain 'S' and resid 2 through 23 removed outlier: 3.938A pdb=" N ILE S 21 " --> pdb=" O GLY S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 41 removed outlier: 4.087A pdb=" N SER S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 59 removed outlier: 3.671A pdb=" N MET S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE S 57 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 86 removed outlier: 3.836A pdb=" N ALA S 75 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 97 removed outlier: 3.690A pdb=" N THR S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 132 removed outlier: 4.554A pdb=" N VAL S 121 " --> pdb=" O ARG S 117 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY S 122 " --> pdb=" O PHE S 118 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE S 123 " --> pdb=" O LEU S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 164 removed outlier: 3.829A pdb=" N VAL S 139 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE S 154 " --> pdb=" O GLN S 150 " (cutoff:3.500A) Proline residue: S 157 - end of helix Processing helix chain 'S' and resid 165 through 175 Processing helix chain 'S' and resid 177 through 189 removed outlier: 3.654A pdb=" N GLY S 189 " --> pdb=" O ALA S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 203 removed outlier: 3.933A pdb=" N GLY S 195 " --> pdb=" O VAL S 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL S 199 " --> pdb=" O GLY S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 219 Processing helix chain 'S' and resid 225 through 246 Processing helix chain 'T' and resid 11 through 23 Processing helix chain 'T' and resid 36 through 51 removed outlier: 3.829A pdb=" N LEU T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) Proline residue: T 45 - end of helix Processing helix chain 'T' and resid 55 through 65 removed outlier: 3.637A pdb=" N HIS T 65 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 91 Processing helix chain 'T' and resid 98 through 121 removed outlier: 4.547A pdb=" N GLN T 102 " --> pdb=" O GLU T 98 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY T 110 " --> pdb=" O VAL T 106 " (cutoff:3.500A) Proline residue: T 111 - end of helix Proline residue: T 118 - end of helix Processing helix chain 'T' and resid 123 through 137 Processing helix chain 'T' and resid 141 through 170 Processing helix chain 'T' and resid 173 through 178 Processing helix chain 'T' and resid 180 through 205 removed outlier: 3.777A pdb=" N ILE T 185 " --> pdb=" O MET T 181 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL T 205 " --> pdb=" O ILE T 201 " (cutoff:3.500A) Processing helix chain 'T' and resid 279 through 283 Processing helix chain 'T' and resid 288 through 301 removed outlier: 4.068A pdb=" N HIS T 292 " --> pdb=" O GLY T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 320 Processing helix chain 'T' and resid 322 through 340 removed outlier: 3.892A pdb=" N LYS T 340 " --> pdb=" O LEU T 336 " (cutoff:3.500A) Processing helix chain 'T' and resid 343 through 362 Processing sheet with id=AA1, first strand: chain 'Z' and resid 215 through 219 removed outlier: 4.412A pdb=" N GLN Z 310 " --> pdb=" O LEU Z 216 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER Z 218 " --> pdb=" O GLN Z 308 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLN Z 308 " --> pdb=" O SER Z 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 256 through 258 removed outlier: 4.172A pdb=" N TRP Z 230 " --> pdb=" O VAL Z 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 245 through 246 removed outlier: 4.297A pdb=" N GLY Z 245 " --> pdb=" O LYS Z 253 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS Z 253 " --> pdb=" O GLY Z 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 215 through 219 removed outlier: 4.403A pdb=" N GLN G 310 " --> pdb=" O LEU G 216 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER G 218 " --> pdb=" O GLN G 308 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN G 308 " --> pdb=" O SER G 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 256 through 258 removed outlier: 4.196A pdb=" N TRP G 230 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 215 through 219 removed outlier: 4.405A pdb=" N GLN T 310 " --> pdb=" O LEU T 216 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER T 218 " --> pdb=" O GLN T 308 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLN T 308 " --> pdb=" O SER T 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 256 through 258 removed outlier: 4.171A pdb=" N TRP T 230 " --> pdb=" O VAL T 238 " (cutoff:3.500A) 919 hydrogen bonds defined for protein. 2727 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: 1.81 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4245 1.34 - 1.46: 2534 1.46 - 1.57: 7017 1.57 - 1.69: 1 1.69 - 1.81: 117 Bond restraints: 13914 Sorted by residual: bond pdb=" CB PRO Z 212 " pdb=" CG PRO Z 212 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.27e+00 bond pdb=" CA ASP Z 232 " pdb=" CB ASP Z 232 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.57e-02 4.06e+03 2.16e+00 bond pdb=" CA GLY Z 263 " pdb=" C GLY Z 263 " ideal model delta sigma weight residual 1.512 1.523 -0.011 8.70e-03 1.32e+04 1.63e+00 bond pdb=" CB PRO Z 220 " pdb=" CG PRO Z 220 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.60e+00 bond pdb=" CB PRO G 212 " pdb=" CG PRO G 212 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.60e+00 ... (remaining 13909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 18712 2.18 - 4.36: 190 4.36 - 6.54: 43 6.54 - 8.72: 1 8.72 - 10.91: 5 Bond angle restraints: 18951 Sorted by residual: angle pdb=" CA PRO Z 212 " pdb=" N PRO Z 212 " pdb=" CD PRO Z 212 " ideal model delta sigma weight residual 112.00 102.02 9.98 1.40e+00 5.10e-01 5.08e+01 angle pdb=" C ASP Z 232 " pdb=" CA ASP Z 232 " pdb=" CB ASP Z 232 " ideal model delta sigma weight residual 110.62 116.24 -5.62 1.51e+00 4.39e-01 1.39e+01 angle pdb=" CA ASP Z 232 " pdb=" CB ASP Z 232 " pdb=" CG ASP Z 232 " ideal model delta sigma weight residual 112.60 115.90 -3.30 1.00e+00 1.00e+00 1.09e+01 angle pdb=" CA LEU Y 147 " pdb=" CB LEU Y 147 " pdb=" CG LEU Y 147 " ideal model delta sigma weight residual 116.30 127.21 -10.91 3.50e+00 8.16e-02 9.71e+00 angle pdb=" CA LEU S 91 " pdb=" CB LEU S 91 " pdb=" CG LEU S 91 " ideal model delta sigma weight residual 116.30 126.92 -10.62 3.50e+00 8.16e-02 9.21e+00 ... (remaining 18946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7144 17.98 - 35.97: 673 35.97 - 53.95: 143 53.95 - 71.93: 47 71.93 - 89.91: 18 Dihedral angle restraints: 8025 sinusoidal: 2961 harmonic: 5064 Sorted by residual: dihedral pdb=" CA PRO Z 212 " pdb=" C PRO Z 212 " pdb=" N ASN Z 213 " pdb=" CA ASN Z 213 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLY Z 211 " pdb=" C GLY Z 211 " pdb=" N PRO Z 212 " pdb=" CA PRO Z 212 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA VAL Z 94 " pdb=" C VAL Z 94 " pdb=" N GLU Z 95 " pdb=" CA GLU Z 95 " ideal model delta harmonic sigma weight residual -180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 8022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1820 0.051 - 0.101: 392 0.101 - 0.152: 52 0.152 - 0.203: 0 0.203 - 0.254: 1 Chirality restraints: 2265 Sorted by residual: chirality pdb=" CA PRO Z 212 " pdb=" N PRO Z 212 " pdb=" C PRO Z 212 " pdb=" CB PRO Z 212 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASP Z 232 " pdb=" N ASP Z 232 " pdb=" C ASP Z 232 " pdb=" CB ASP Z 232 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CG LEU Y 50 " pdb=" CB LEU Y 50 " pdb=" CD1 LEU Y 50 " pdb=" CD2 LEU Y 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2262 not shown) Planarity restraints: 2349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Z 219 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO Z 220 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO Z 220 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO Z 220 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 219 " 0.062 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO G 220 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO G 220 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 220 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS T 219 " -0.058 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO T 220 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO T 220 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO T 220 " -0.047 5.00e-02 4.00e+02 ... (remaining 2346 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 324 2.70 - 3.25: 14250 3.25 - 3.80: 22563 3.80 - 4.35: 28574 4.35 - 4.90: 48216 Nonbonded interactions: 113927 Sorted by model distance: nonbonded pdb=" O PHE Z 158 " pdb=" OG1 THR Z 162 " model vdw 2.148 3.040 nonbonded pdb=" O PHE G 158 " pdb=" OG1 THR G 162 " model vdw 2.167 3.040 nonbonded pdb=" O PHE T 158 " pdb=" OG1 THR T 162 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASP Z 117 " pdb=" O4 MAN Z 401 " model vdw 2.238 3.040 nonbonded pdb=" O ASN S 63 " pdb=" O2 MAN T 401 " model vdw 2.246 3.040 ... (remaining 113922 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: 0.03 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'S' selection = chain 'Y' } ncs_group { reference = chain 'G' selection = chain 'T' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.960 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.003 0.135 13914 Z= 0.132 Angle : 0.588 10.906 18951 Z= 0.303 Chirality : 0.040 0.254 2265 Planarity : 0.006 0.107 2349 Dihedral : 16.079 89.915 4809 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.75 % Favored : 93.92 % Rotamer: Outliers : 2.16 % Allowed : 15.95 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1809 helix: 1.89 (0.15), residues: 1224 sheet: -2.27 (0.84), residues: 30 loop : -1.74 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 153 TYR 0.006 0.001 TYR G 167 PHE 0.009 0.001 PHE G 330 TRP 0.027 0.001 TRP T 334 HIS 0.003 0.001 HIS Y 93 Details of bonding type rmsd covalent geometry : bond 0.00304 (13914) covalent geometry : angle 0.58812 (18951) hydrogen bonds : bond 0.10403 ( 919) hydrogen bonds : angle 4.58941 ( 2727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.441 Fit side-chains REVERT: F 63 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7747 (p0) outliers start: 30 outliers final: 24 residues processed: 185 average time/residue: 0.4454 time to fit residues: 92.2144 Evaluate side-chains 180 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 171 THR Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 311 SER Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 251 VAL Chi-restraints excluded: chain T residue 266 ASN Chi-restraints excluded: chain T residue 268 VAL Chi-restraints excluded: chain T residue 278 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 242 ASN ** Z 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN S 242 ASN T 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.163271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134836 restraints weight = 17643.105| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.85 r_work: 0.3451 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13914 Z= 0.146 Angle : 0.558 8.633 18951 Z= 0.290 Chirality : 0.040 0.151 2265 Planarity : 0.006 0.082 2349 Dihedral : 5.111 53.726 1976 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.30 % Favored : 93.31 % Rotamer: Outliers : 3.30 % Allowed : 15.09 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1809 helix: 1.88 (0.15), residues: 1230 sheet: -2.16 (0.83), residues: 30 loop : -1.82 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Z 125 TYR 0.008 0.001 TYR G 167 PHE 0.012 0.001 PHE G 330 TRP 0.015 0.001 TRP T 334 HIS 0.003 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00336 (13914) covalent geometry : angle 0.55760 (18951) hydrogen bonds : bond 0.04524 ( 919) hydrogen bonds : angle 4.04866 ( 2727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.519 Fit side-chains REVERT: Y 44 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8237 (ttp) REVERT: Y 203 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.6073 (pmm) REVERT: Z 86 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8521 (mp) REVERT: Z 95 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6830 (tp30) REVERT: F 63 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8203 (p0) REVERT: F 203 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.6793 (ppp) REVERT: G 86 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8406 (mp) REVERT: T 94 VAL cc_start: 0.6038 (OUTLIER) cc_final: 0.5768 (t) REVERT: T 169 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8211 (mm-40) outliers start: 46 outliers final: 14 residues processed: 198 average time/residue: 0.4403 time to fit residues: 98.1900 Evaluate side-chains 186 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 23 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 95 GLU Chi-restraints excluded: chain Z residue 171 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain S residue 63 ASN Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 94 VAL Chi-restraints excluded: chain T residue 169 GLN Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 309 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 51 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 242 ASN Z 70 ASN F 29 GLN F 242 ASN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.165033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136960 restraints weight = 17618.318| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.90 r_work: 0.3461 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13914 Z= 0.121 Angle : 0.527 10.036 18951 Z= 0.272 Chirality : 0.039 0.147 2265 Planarity : 0.005 0.081 2349 Dihedral : 4.429 41.316 1953 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.97 % Favored : 93.70 % Rotamer: Outliers : 3.30 % Allowed : 15.88 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1809 helix: 1.97 (0.15), residues: 1227 sheet: -2.11 (0.83), residues: 30 loop : -1.81 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 125 TYR 0.008 0.001 TYR G 167 PHE 0.010 0.001 PHE G 330 TRP 0.012 0.001 TRP T 334 HIS 0.003 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00265 (13914) covalent geometry : angle 0.52720 (18951) hydrogen bonds : bond 0.04171 ( 919) hydrogen bonds : angle 3.95948 ( 2727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.535 Fit side-chains REVERT: Y 29 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8485 (mm110) REVERT: Y 44 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8240 (ttp) REVERT: Y 201 ASN cc_start: 0.8599 (t0) cc_final: 0.8244 (t0) REVERT: Y 203 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.6061 (pmm) REVERT: Z 86 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8474 (mp) REVERT: F 63 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8175 (p0) REVERT: F 203 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.6741 (ppp) REVERT: G 86 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8387 (mp) REVERT: G 98 GLU cc_start: 0.5760 (tt0) cc_final: 0.5522 (tt0) REVERT: G 125 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8583 (ttt180) REVERT: S 1 MET cc_start: 0.5415 (ttp) cc_final: 0.5209 (ttp) REVERT: T 86 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8388 (mp) REVERT: T 169 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8203 (mm-40) outliers start: 46 outliers final: 18 residues processed: 202 average time/residue: 0.4305 time to fit residues: 97.8929 Evaluate side-chains 190 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 171 THR Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain S residue 63 ASN Chi-restraints excluded: chain S residue 203 MET Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 169 GLN Chi-restraints excluded: chain T residue 251 VAL Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 309 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 68 optimal weight: 0.9990 chunk 161 optimal weight: 0.0060 chunk 159 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 88 ASN Y 242 ASN ** Z 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 242 ASN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN S 242 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138364 restraints weight = 17664.481| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.90 r_work: 0.3475 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13914 Z= 0.119 Angle : 0.523 9.677 18951 Z= 0.270 Chirality : 0.039 0.139 2265 Planarity : 0.005 0.078 2349 Dihedral : 4.333 44.118 1950 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 3.95 % Allowed : 16.09 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1809 helix: 2.05 (0.15), residues: 1224 sheet: -2.15 (0.84), residues: 30 loop : -1.84 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 125 TYR 0.006 0.001 TYR G 167 PHE 0.009 0.001 PHE Z 330 TRP 0.011 0.001 TRP T 334 HIS 0.002 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00258 (13914) covalent geometry : angle 0.52317 (18951) hydrogen bonds : bond 0.04036 ( 919) hydrogen bonds : angle 3.92391 ( 2727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.512 Fit side-chains REVERT: Y 201 ASN cc_start: 0.8577 (t0) cc_final: 0.8237 (t0) REVERT: Y 203 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.6072 (pmm) REVERT: Z 86 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8476 (mp) REVERT: F 63 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8240 (p0) REVERT: F 203 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.6798 (ppp) REVERT: G 98 GLU cc_start: 0.5699 (tt0) cc_final: 0.5473 (tt0) REVERT: G 181 MET cc_start: 0.7471 (ptm) cc_final: 0.7165 (ptt) REVERT: G 206 ASN cc_start: 0.8111 (p0) cc_final: 0.7907 (p0) REVERT: G 232 ASP cc_start: 0.7607 (p0) cc_final: 0.7351 (p0) REVERT: T 86 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8381 (mp) REVERT: T 169 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8228 (mm-40) outliers start: 55 outliers final: 24 residues processed: 204 average time/residue: 0.4579 time to fit residues: 104.8460 Evaluate side-chains 197 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 23 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain S residue 63 ASN Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 169 GLN Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 251 VAL Chi-restraints excluded: chain T residue 268 VAL Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 309 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 0.0010 chunk 23 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 242 ASN ** Z 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN F 174 ASN F 242 ASN S 29 GLN S 88 ASN S 174 ASN S 242 ASN T 26 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.165869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137621 restraints weight = 17741.111| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.88 r_work: 0.3485 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13914 Z= 0.115 Angle : 0.522 9.941 18951 Z= 0.270 Chirality : 0.039 0.133 2265 Planarity : 0.005 0.075 2349 Dihedral : 4.268 43.917 1949 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.97 % Favored : 93.70 % Rotamer: Outliers : 3.52 % Allowed : 16.88 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1809 helix: 2.09 (0.15), residues: 1224 sheet: -2.07 (0.83), residues: 30 loop : -1.83 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 125 TYR 0.013 0.001 TYR Z 51 PHE 0.008 0.001 PHE Z 330 TRP 0.012 0.001 TRP T 334 HIS 0.003 0.001 HIS S 93 Details of bonding type rmsd covalent geometry : bond 0.00249 (13914) covalent geometry : angle 0.52177 (18951) hydrogen bonds : bond 0.03904 ( 919) hydrogen bonds : angle 3.89643 ( 2727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.517 Fit side-chains REVERT: Y 201 ASN cc_start: 0.8565 (t0) cc_final: 0.8211 (t0) REVERT: Y 203 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.5983 (pmm) REVERT: F 63 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8212 (p0) REVERT: F 203 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.6805 (ppp) REVERT: G 98 GLU cc_start: 0.5698 (tt0) cc_final: 0.5483 (tt0) REVERT: G 181 MET cc_start: 0.7471 (ptm) cc_final: 0.7156 (ptt) REVERT: G 232 ASP cc_start: 0.7547 (p0) cc_final: 0.7264 (p0) REVERT: S 149 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7456 (mp) REVERT: T 169 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8275 (mm-40) outliers start: 49 outliers final: 28 residues processed: 200 average time/residue: 0.4375 time to fit residues: 98.6633 Evaluate side-chains 196 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 23 MET Chi-restraints excluded: chain Z residue 171 THR Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain S residue 63 ASN Chi-restraints excluded: chain S residue 88 ASN Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain T residue 169 GLN Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 251 VAL Chi-restraints excluded: chain T residue 268 VAL Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 309 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 29 GLN Y 242 ASN ** Z 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 242 ASN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN S 242 ASN T 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.165084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136938 restraints weight = 17620.929| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.85 r_work: 0.3471 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13914 Z= 0.131 Angle : 0.534 9.511 18951 Z= 0.277 Chirality : 0.039 0.141 2265 Planarity : 0.005 0.074 2349 Dihedral : 4.304 44.867 1949 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.36 % Favored : 93.31 % Rotamer: Outliers : 3.52 % Allowed : 16.95 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1809 helix: 2.02 (0.15), residues: 1227 sheet: -2.12 (0.83), residues: 30 loop : -1.84 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 153 TYR 0.010 0.001 TYR Z 51 PHE 0.010 0.001 PHE G 330 TRP 0.012 0.001 TRP T 334 HIS 0.004 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00300 (13914) covalent geometry : angle 0.53352 (18951) hydrogen bonds : bond 0.04057 ( 919) hydrogen bonds : angle 3.93011 ( 2727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.520 Fit side-chains REVERT: Y 201 ASN cc_start: 0.8584 (t0) cc_final: 0.8252 (t0) REVERT: Y 203 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.5971 (pmm) REVERT: F 29 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: F 63 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8202 (p0) REVERT: F 203 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.6794 (ppp) REVERT: G 232 ASP cc_start: 0.7457 (p0) cc_final: 0.7182 (OUTLIER) REVERT: S 178 ASP cc_start: 0.6975 (t70) cc_final: 0.6645 (t0) REVERT: T 285 THR cc_start: 0.7817 (m) cc_final: 0.7539 (t) outliers start: 49 outliers final: 31 residues processed: 197 average time/residue: 0.4593 time to fit residues: 101.7739 Evaluate side-chains 198 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 23 MET Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 171 THR Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain S residue 63 ASN Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 251 VAL Chi-restraints excluded: chain T residue 268 VAL Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 309 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 172 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 167 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 242 ASN F 174 ASN F 242 ASN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN S 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.165274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137168 restraints weight = 17586.237| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.86 r_work: 0.3474 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13914 Z= 0.127 Angle : 0.538 9.999 18951 Z= 0.280 Chirality : 0.039 0.139 2265 Planarity : 0.005 0.074 2349 Dihedral : 4.310 44.296 1949 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.25 % Favored : 93.42 % Rotamer: Outliers : 3.38 % Allowed : 17.39 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1809 helix: 2.02 (0.15), residues: 1227 sheet: -2.20 (0.82), residues: 30 loop : -1.83 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 125 TYR 0.008 0.001 TYR G 167 PHE 0.010 0.001 PHE G 330 TRP 0.018 0.001 TRP T 334 HIS 0.004 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00290 (13914) covalent geometry : angle 0.53833 (18951) hydrogen bonds : bond 0.04043 ( 919) hydrogen bonds : angle 3.94850 ( 2727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.534 Fit side-chains REVERT: Y 201 ASN cc_start: 0.8568 (t0) cc_final: 0.8228 (t0) REVERT: Y 203 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.5967 (pmm) REVERT: F 29 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: F 63 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8224 (p0) REVERT: F 203 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.6794 (ppp) REVERT: G 181 MET cc_start: 0.7459 (ptm) cc_final: 0.7140 (ptt) REVERT: S 149 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7497 (mp) REVERT: S 178 ASP cc_start: 0.6940 (t70) cc_final: 0.6601 (t0) REVERT: T 285 THR cc_start: 0.7807 (m) cc_final: 0.7533 (t) outliers start: 47 outliers final: 30 residues processed: 195 average time/residue: 0.4606 time to fit residues: 101.2021 Evaluate side-chains 200 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 23 MET Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 171 THR Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain S residue 63 ASN Chi-restraints excluded: chain S residue 88 ASN Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 251 VAL Chi-restraints excluded: chain T residue 268 VAL Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 309 THR Chi-restraints excluded: chain T residue 352 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 168 optimal weight: 0.0040 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 242 ASN ** Z 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 242 ASN G 206 ASN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN S 242 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137691 restraints weight = 17498.424| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.84 r_work: 0.3487 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13914 Z= 0.119 Angle : 0.533 9.672 18951 Z= 0.277 Chirality : 0.039 0.132 2265 Planarity : 0.005 0.073 2349 Dihedral : 4.303 45.468 1949 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.52 % Favored : 93.15 % Rotamer: Outliers : 3.16 % Allowed : 17.82 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1809 helix: 2.06 (0.15), residues: 1227 sheet: -2.16 (0.82), residues: 30 loop : -1.83 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 125 TYR 0.007 0.001 TYR G 167 PHE 0.022 0.001 PHE S 89 TRP 0.021 0.001 TRP T 334 HIS 0.005 0.001 HIS S 93 Details of bonding type rmsd covalent geometry : bond 0.00264 (13914) covalent geometry : angle 0.53304 (18951) hydrogen bonds : bond 0.03925 ( 919) hydrogen bonds : angle 3.93220 ( 2727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.506 Fit side-chains REVERT: Y 201 ASN cc_start: 0.8574 (t0) cc_final: 0.8228 (t0) REVERT: Y 203 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.5946 (pmm) REVERT: F 29 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8001 (mp10) REVERT: F 63 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8220 (p0) REVERT: F 203 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.6812 (ppp) REVERT: G 181 MET cc_start: 0.7413 (ptm) cc_final: 0.7086 (ptt) REVERT: S 178 ASP cc_start: 0.6890 (t70) cc_final: 0.6555 (t0) REVERT: T 285 THR cc_start: 0.7945 (m) cc_final: 0.7656 (t) outliers start: 44 outliers final: 31 residues processed: 197 average time/residue: 0.4447 time to fit residues: 98.8936 Evaluate side-chains 202 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 23 MET Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 171 THR Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain S residue 63 ASN Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 251 VAL Chi-restraints excluded: chain T residue 268 VAL Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 309 THR Chi-restraints excluded: chain T residue 352 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 4.9990 chunk 178 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 81 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 242 ASN ** Z 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 242 ASN G 206 ASN S 29 GLN S 88 ASN S 242 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.166185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137975 restraints weight = 17563.862| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.86 r_work: 0.3491 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 13914 Z= 0.121 Angle : 0.540 10.080 18951 Z= 0.281 Chirality : 0.039 0.132 2265 Planarity : 0.005 0.072 2349 Dihedral : 4.298 45.042 1949 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.19 % Favored : 93.48 % Rotamer: Outliers : 3.16 % Allowed : 18.03 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1809 helix: 2.08 (0.15), residues: 1224 sheet: -2.14 (0.83), residues: 30 loop : -1.86 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 125 TYR 0.007 0.001 TYR G 167 PHE 0.012 0.001 PHE S 145 TRP 0.023 0.001 TRP T 334 HIS 0.005 0.001 HIS S 93 Details of bonding type rmsd covalent geometry : bond 0.00273 (13914) covalent geometry : angle 0.53992 (18951) hydrogen bonds : bond 0.03891 ( 919) hydrogen bonds : angle 3.92037 ( 2727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.620 Fit side-chains REVERT: Y 201 ASN cc_start: 0.8544 (t0) cc_final: 0.8209 (t0) REVERT: Y 203 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.5967 (pmm) REVERT: F 63 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8238 (p0) REVERT: F 203 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.6829 (ppp) REVERT: S 63 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8060 (p0) REVERT: S 178 ASP cc_start: 0.6894 (t70) cc_final: 0.6561 (t0) REVERT: T 98 GLU cc_start: 0.5885 (tt0) cc_final: 0.5632 (tt0) REVERT: T 285 THR cc_start: 0.7912 (m) cc_final: 0.7622 (t) outliers start: 44 outliers final: 30 residues processed: 193 average time/residue: 0.4570 time to fit residues: 99.1125 Evaluate side-chains 204 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 23 MET Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 171 THR Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain S residue 63 ASN Chi-restraints excluded: chain S residue 88 ASN Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 251 VAL Chi-restraints excluded: chain T residue 268 VAL Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 309 THR Chi-restraints excluded: chain T residue 352 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 43 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN Y 242 ASN ** Z 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 242 ASN G 206 ASN S 29 GLN S 88 ASN S 242 ASN T 102 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137854 restraints weight = 17627.214| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.87 r_work: 0.3491 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13914 Z= 0.121 Angle : 0.539 9.606 18951 Z= 0.280 Chirality : 0.039 0.130 2265 Planarity : 0.005 0.071 2349 Dihedral : 4.296 46.018 1949 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.41 % Favored : 93.37 % Rotamer: Outliers : 2.95 % Allowed : 18.32 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1809 helix: 2.06 (0.15), residues: 1227 sheet: -2.10 (0.83), residues: 30 loop : -1.84 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 153 TYR 0.007 0.001 TYR T 51 PHE 0.009 0.001 PHE Y 145 TRP 0.025 0.001 TRP T 334 HIS 0.005 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00269 (13914) covalent geometry : angle 0.53911 (18951) hydrogen bonds : bond 0.03900 ( 919) hydrogen bonds : angle 3.92101 ( 2727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.528 Fit side-chains REVERT: Y 201 ASN cc_start: 0.8543 (t0) cc_final: 0.8193 (t0) REVERT: Y 203 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.5952 (pmm) REVERT: F 63 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8216 (p0) REVERT: F 203 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.6824 (ppp) REVERT: G 181 MET cc_start: 0.7474 (ptm) cc_final: 0.7152 (ptt) REVERT: S 63 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8050 (p0) REVERT: S 178 ASP cc_start: 0.6907 (t70) cc_final: 0.6575 (t0) REVERT: T 98 GLU cc_start: 0.5898 (tt0) cc_final: 0.5636 (tt0) REVERT: T 285 THR cc_start: 0.7906 (m) cc_final: 0.7618 (t) outliers start: 41 outliers final: 30 residues processed: 193 average time/residue: 0.4636 time to fit residues: 100.5893 Evaluate side-chains 203 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 88 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 23 MET Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 171 THR Chi-restraints excluded: chain Z residue 251 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain S residue 63 ASN Chi-restraints excluded: chain S residue 88 ASN Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 206 ASN Chi-restraints excluded: chain T residue 251 VAL Chi-restraints excluded: chain T residue 268 VAL Chi-restraints excluded: chain T residue 278 VAL Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 309 THR Chi-restraints excluded: chain T residue 352 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 94 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN Y 242 ASN ** Z 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN G 206 ASN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN S 242 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.165522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137241 restraints weight = 17697.309| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.82 r_work: 0.3485 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 13914 Z= 0.229 Angle : 0.937 59.195 18951 Z= 0.575 Chirality : 0.043 0.484 2265 Planarity : 0.005 0.071 2349 Dihedral : 4.294 46.036 1949 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.63 % Favored : 93.20 % Rotamer: Outliers : 2.87 % Allowed : 18.39 % Favored : 78.74 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1809 helix: 2.03 (0.15), residues: 1227 sheet: -2.07 (0.83), residues: 30 loop : -1.84 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 153 TYR 0.006 0.001 TYR G 167 PHE 0.018 0.001 PHE Y 89 TRP 0.023 0.001 TRP T 334 HIS 0.005 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00464 (13914) covalent geometry : angle 0.93659 (18951) hydrogen bonds : bond 0.03980 ( 919) hydrogen bonds : angle 3.92520 ( 2727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4834.38 seconds wall clock time: 83 minutes 11.42 seconds (4991.42 seconds total)