Starting phenix.real_space_refine on Tue Aug 26 00:27:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kg3_62307/08_2025/9kg3_62307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kg3_62307/08_2025/9kg3_62307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kg3_62307/08_2025/9kg3_62307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kg3_62307/08_2025/9kg3_62307.map" model { file = "/net/cci-nas-00/data/ceres_data/9kg3_62307/08_2025/9kg3_62307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kg3_62307/08_2025/9kg3_62307.cif" } resolution = 3.07 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= 0.062 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: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 10310 2.51 5 N 2809 2.21 5 O 3256 1.98 5 H 15834 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32258 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4590 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "B" Number of atoms: 4615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4615 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "C" Number of atoms: 4615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4615 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "D" Number of atoms: 4615 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 4593 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Conformer: "B" Number of residues, atoms: 293, 4593 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} bond proxies already assigned to first conformer: 4622 Chain: "E" Number of atoms: 4615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4615 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "F" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4604 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Chain: "G" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4604 Classifications: {'peptide': 293} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS D 46 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS D 46 " occ=0.50 Time building chain proxies: 6.71, per 1000 atoms: 0.21 Number of scatterers: 32258 At special positions: 0 Unit cell: (111.32, 112.24, 115.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 3256 8.00 N 2809 7.00 C 10310 6.00 H 15834 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 24 sheets defined 3.7% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.884A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 Processing helix chain 'B' and resid 217 through 223 removed outlier: 4.079A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.829A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 6 removed outlier: 3.722A pdb=" N ILE D 5 " --> pdb=" O ASP D 2 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN D 6 " --> pdb=" O SER D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 223 removed outlier: 4.137A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 6 removed outlier: 3.713A pdb=" N ILE E 5 " --> pdb=" O ASP E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.064A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 217 through 223 removed outlier: 4.130A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 223 removed outlier: 4.029A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 29 removed outlier: 3.695A pdb=" N ASP A 29 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA A 229 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR A 101 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 231 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 69 removed outlier: 3.527A pdb=" N TYR A 68 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 75 through 89 current: chain 'A' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 164 through 171 current: chain 'A' and resid 265 through 270 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 265 through 270 current: chain 'A' and resid 290 through 292 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 113 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 109 through 113 current: chain 'A' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 133 through 149 current: chain 'B' and resid 133 through 137 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 133 through 137 current: chain 'C' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 133 through 149 current: chain 'D' and resid 132 through 149 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 132 through 149 current: chain 'E' and resid 133 through 135 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 133 through 135 current: chain 'F' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 133 through 149 current: chain 'G' and resid 133 through 149 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 21 through 22 removed outlier: 3.550A pdb=" N ILE B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 229 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR B 101 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 231 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 69 removed outlier: 3.566A pdb=" N ARG B 66 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR B 68 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 75 through 89 current: chain 'B' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 164 through 171 current: chain 'B' and resid 265 through 270 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 265 through 270 current: chain 'B' and resid 290 through 291 Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 176 removed outlier: 3.532A pdb=" N MET B 174 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASN B 176 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 27 removed outlier: 3.622A pdb=" N LYS C 21 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 40 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE C 39 " --> pdb=" O ARG C 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 89 current: chain 'C' and resid 165 through 171 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 165 through 171 current: chain 'C' and resid 265 through 276 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 265 through 276 current: chain 'C' and resid 290 through 291 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 21 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 22 current: chain 'D' and resid 34 through 43 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 56 current: chain 'D' and resid 229 through 234 Processing sheet with id=AB4, first strand: chain 'D' and resid 70 through 71 removed outlier: 3.575A pdb=" N LYS D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 75 through 89 current: chain 'D' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 164 through 171 current: chain 'D' and resid 265 through 270 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 265 through 270 current: chain 'D' and resid 290 through 291 Processing sheet with id=AB5, first strand: chain 'E' and resid 20 through 27 removed outlier: 3.604A pdb=" N ILE E 43 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA E 229 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR E 101 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL E 231 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 89 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 79 through 89 current: chain 'E' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 164 through 171 current: chain 'E' and resid 275 through 276 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 276 current: chain 'E' and resid 290 through 292 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AB9, first strand: chain 'F' and resid 21 through 22 removed outlier: 3.593A pdb=" N LYS F 21 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 52 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA F 229 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR F 101 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL F 231 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 26 through 28 Processing sheet with id=AC2, first strand: chain 'F' and resid 153 through 158 removed outlier: 4.376A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS F 75 " --> pdb=" O TRP F 260 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TRP F 260 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLY F 77 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU F 258 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ALA F 79 " --> pdb=" O TYR F 256 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR F 256 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP F 254 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE F 284 " --> pdb=" O THR F 243 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP F 276 " --> pdb=" O ARG F 251 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP F 274 " --> pdb=" O ARG F 253 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP F 255 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASP F 272 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N GLN F 257 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR F 270 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N HIS F 259 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N THR F 268 " --> pdb=" O HIS F 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AC4, first strand: chain 'G' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 20 through 22 current: chain 'G' and resid 36 through 43 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 56 current: chain 'G' and resid 229 through 234 Processing sheet with id=AC5, first strand: chain 'G' and resid 70 through 71 removed outlier: 3.631A pdb=" N GLU G 71 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 75 through 89 current: chain 'G' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 164 through 171 current: chain 'G' and resid 265 through 271 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 242 through 245 removed outlier: 3.660A pdb=" N ILE G 284 " --> pdb=" O THR G 243 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 420 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: 7.32 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15834 1.03 - 1.22: 1 1.22 - 1.42: 7211 1.42 - 1.61: 9479 1.61 - 1.81: 98 Bond restraints: 32623 Sorted by residual: bond pdb=" CA TRP G 80 " pdb=" C TRP G 80 " ideal model delta sigma weight residual 1.520 1.543 -0.022 1.02e-02 9.61e+03 4.84e+00 bond pdb=" C TRP G 80 " pdb=" O TRP G 80 " ideal model delta sigma weight residual 1.237 1.218 0.019 1.05e-02 9.07e+03 3.40e+00 bond pdb=" CA TRP E 80 " pdb=" C TRP E 80 " ideal model delta sigma weight residual 1.520 1.502 0.019 1.02e-02 9.61e+03 3.32e+00 bond pdb=" N TYR D 102 " pdb=" CA TYR D 102 " ideal model delta sigma weight residual 1.463 1.453 0.011 6.90e-03 2.10e+04 2.33e+00 bond pdb=" C TRP E 80 " pdb=" N PRO E 81 " ideal model delta sigma weight residual 1.335 1.345 -0.010 8.70e-03 1.32e+04 1.28e+00 ... (remaining 32618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 57765 1.36 - 2.71: 858 2.71 - 4.07: 72 4.07 - 5.42: 5 5.42 - 6.78: 1 Bond angle restraints: 58701 Sorted by residual: angle pdb=" N ILE E 5 " pdb=" CA ILE E 5 " pdb=" C ILE E 5 " ideal model delta sigma weight residual 112.29 107.73 4.56 9.40e-01 1.13e+00 2.36e+01 angle pdb=" O TRP G 80 " pdb=" C TRP G 80 " pdb=" N PRO G 81 " ideal model delta sigma weight residual 121.88 123.83 -1.95 7.10e-01 1.98e+00 7.54e+00 angle pdb=" N VAL B 190 " pdb=" CA VAL B 190 " pdb=" C VAL B 190 " ideal model delta sigma weight residual 111.62 109.50 2.12 7.90e-01 1.60e+00 7.18e+00 angle pdb=" O TRP E 80 " pdb=" C TRP E 80 " pdb=" N PRO E 81 " ideal model delta sigma weight residual 121.88 120.16 1.72 7.10e-01 1.98e+00 5.89e+00 angle pdb=" CA GLY A 122 " pdb=" C GLY A 122 " pdb=" N ASN A 123 " ideal model delta sigma weight residual 114.56 117.27 -2.71 1.22e+00 6.72e-01 4.94e+00 ... (remaining 58696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 14565 17.71 - 35.41: 566 35.41 - 53.12: 212 53.12 - 70.82: 62 70.82 - 88.53: 4 Dihedral angle restraints: 15409 sinusoidal: 8307 harmonic: 7102 Sorted by residual: dihedral pdb=" N LEU C 52 " pdb=" CA LEU C 52 " pdb=" CB LEU C 52 " pdb=" CG LEU C 52 " ideal model delta sinusoidal sigma weight residual -60.00 -116.63 56.63 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CA ARG A 253 " pdb=" CB ARG A 253 " pdb=" CG ARG A 253 " pdb=" CD ARG A 253 " ideal model delta sinusoidal sigma weight residual -180.00 -126.69 -53.31 3 1.50e+01 4.44e-03 9.19e+00 dihedral pdb=" N ARG F 251 " pdb=" CA ARG F 251 " pdb=" CB ARG F 251 " pdb=" CG ARG F 251 " ideal model delta sinusoidal sigma weight residual 60.00 112.88 -52.88 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 15406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1494 0.028 - 0.055: 628 0.055 - 0.083: 90 0.083 - 0.110: 139 0.110 - 0.138: 79 Chirality restraints: 2430 Sorted by residual: chirality pdb=" CA ILE D 98 " pdb=" N ILE D 98 " pdb=" C ILE D 98 " pdb=" CB ILE D 98 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE F 136 " pdb=" N ILE F 136 " pdb=" C ILE F 136 " pdb=" CB ILE F 136 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE B 98 " pdb=" N ILE B 98 " pdb=" C ILE B 98 " pdb=" CB ILE B 98 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 2427 not shown) Planarity restraints: 4918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 102 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 103 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 180 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 181 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 225 " 0.017 5.00e-02 4.00e+02 2.53e-02 1.02e+00 pdb=" N PRO D 226 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO D 226 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 226 " 0.014 5.00e-02 4.00e+02 ... (remaining 4915 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 507 2.05 - 2.69: 50118 2.69 - 3.32: 88597 3.32 - 3.96: 117002 3.96 - 4.60: 183296 Nonbonded interactions: 439520 Sorted by model distance: nonbonded pdb=" HE2 TYR G 191 " pdb=" HD3 ARG G 200 " model vdw 1.411 2.270 nonbonded pdb=" HE2 TYR E 191 " pdb=" HD3 ARG E 200 " model vdw 1.489 2.270 nonbonded pdb=" HE2 TYR A 191 " pdb=" HD3 ARG A 200 " model vdw 1.506 2.270 nonbonded pdb=" OD1 ASP E 100 " pdb=" H TYR E 101 " model vdw 1.553 2.450 nonbonded pdb=" H HIS D 259 " pdb=" O LYS D 266 " model vdw 1.557 2.450 ... (remaining 439515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 45 or resid 47 through 239 or (resid 240 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ or name H or name HA )) or resid 241 through 282 or (resid 283 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE o \ r name NZ or name H or name HA )) or resid 284 through 293)) selection = (chain 'B' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 45 or resid 47 through 65 or (resid 66 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA )) or resid 67 through 74 or \ (resid 75 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA )) or resid 76 through 239 or \ (resid 240 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA )) or resid 241 through 261 or \ (resid 262 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or resid 263 through 282 or (resid 283 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name CE or name NZ or \ name H or name HA )) or resid 284 through 293)) selection = (chain 'C' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 45 or resid 47 through 65 or (resid 66 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA )) or resid 67 through 74 or \ (resid 75 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA )) or resid 76 through 239 or \ (resid 240 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA )) or resid 241 through 261 or \ (resid 262 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or resid 263 through 282 or (resid 283 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name CE or name NZ or \ name H or name HA )) or resid 284 through 293)) selection = (chain 'D' and (resid 1 through 45 or resid 47 through 65 or (resid 66 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2 or name H or name HA )) or resid 67 through 74 \ or (resid 75 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name CE or name NZ or name H or name HA )) or resid 76 through 261 o \ r (resid 262 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or resid 263 through 282 or (resid 283 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name CE or name NZ o \ r name H or name HA )) or resid 284 through 293)) selection = (chain 'E' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 45 or resid 47 through 65 or (resid 66 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA )) or resid 67 through 74 or \ (resid 75 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA )) or resid 76 through 239 or \ (resid 240 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA )) or resid 241 through 261 or \ (resid 262 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or resid 263 through 282 or (resid 283 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name CE or name NZ or \ name H or name HA )) or resid 284 through 293)) selection = (chain 'F' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 31 through 45 or resid 47 through 65 or (resid 66 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA )) or resid 67 through 74 or \ (resid 75 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA )) or resid 76 through 239 or \ (resid 240 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA )) or resid 241 through 261 or \ (resid 262 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or resid 263 through 293)) selection = (chain 'G' and (resid 1 through 45 or resid 47 through 65 or (resid 66 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2 or name H or name HA )) or resid 67 through 74 \ or (resid 75 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name CE or name NZ or name H or name HA )) or resid 76 through 239 o \ r (resid 240 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name CE or name NZ or name H or name HA )) or resid 241 through 261 \ or (resid 262 and (name N or name CA or name C or name O or name CB or name OG o \ r name H or name HA )) or resid 263 through 282 or (resid 283 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name CE or name NZ \ or name H or name HA )) or resid 284 through 293)) } 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=0.50 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: 1.480 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: 0.200 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.840 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 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 : 0.002 0.038 16789 Z= 0.125 Angle : 0.434 6.778 22729 Z= 0.243 Chirality : 0.041 0.138 2430 Planarity : 0.002 0.031 2935 Dihedral : 9.071 88.527 6180 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 0.50 % Allowed : 4.08 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -0.86 (0.19), residues: 2040 helix: -0.53 (0.71), residues: 42 sheet: -0.34 (0.17), residues: 1107 loop : -0.72 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.012 0.001 TYR A 102 PHE 0.006 0.001 PHE B 196 TRP 0.006 0.001 TRP D 260 HIS 0.003 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00249 (16789) covalent geometry : angle 0.43428 (22729) hydrogen bonds : bond 0.26766 ( 177) hydrogen bonds : angle 12.83860 ( 420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 680 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 671 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8256 (mttm) cc_final: 0.8016 (mtpt) REVERT: A 29 ASP cc_start: 0.7321 (t0) cc_final: 0.6975 (t0) REVERT: A 34 MET cc_start: 0.7764 (mtm) cc_final: 0.6281 (ptp) REVERT: A 44 ASP cc_start: 0.7318 (t0) cc_final: 0.6996 (t70) REVERT: A 46 LYS cc_start: 0.7664 (ptpp) cc_final: 0.7169 (pttp) REVERT: A 111 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 118 TYR cc_start: 0.7844 (p90) cc_final: 0.7248 (p90) REVERT: A 140 VAL cc_start: 0.8105 (t) cc_final: 0.7894 (p) REVERT: A 164 LYS cc_start: 0.7775 (tttm) cc_final: 0.7397 (tptp) REVERT: A 183 ASP cc_start: 0.8137 (p0) cc_final: 0.7810 (p0) REVERT: A 200 ARG cc_start: 0.7029 (mtt180) cc_final: 0.6764 (mtt180) REVERT: A 227 ASP cc_start: 0.6575 (t0) cc_final: 0.6032 (m-30) REVERT: A 237 LYS cc_start: 0.7507 (pttp) cc_final: 0.7297 (pttm) REVERT: B 29 ASP cc_start: 0.7545 (t0) cc_final: 0.6973 (t0) REVERT: B 31 GLU cc_start: 0.6459 (tp30) cc_final: 0.6221 (mp0) REVERT: B 46 LYS cc_start: 0.8337 (pttm) cc_final: 0.7656 (mmmt) REVERT: B 106 SER cc_start: 0.8637 (p) cc_final: 0.8340 (m) REVERT: B 124 VAL cc_start: 0.6862 (t) cc_final: 0.6632 (p) REVERT: B 164 LYS cc_start: 0.8311 (ptmm) cc_final: 0.8085 (ptmm) REVERT: B 183 ASP cc_start: 0.7464 (t70) cc_final: 0.7028 (m-30) REVERT: B 227 ASP cc_start: 0.6650 (t0) cc_final: 0.6005 (m-30) REVERT: B 233 THR cc_start: 0.8341 (p) cc_final: 0.8099 (p) REVERT: B 237 LYS cc_start: 0.6845 (mtmm) cc_final: 0.6522 (mmtm) REVERT: B 250 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6810 (mt-10) REVERT: B 287 GLU cc_start: 0.6690 (tp30) cc_final: 0.6424 (tt0) REVERT: B 288 LYS cc_start: 0.7050 (mtmt) cc_final: 0.6738 (mmtt) REVERT: C 21 LYS cc_start: 0.8047 (tppt) cc_final: 0.7448 (mmmm) REVERT: C 41 SER cc_start: 0.9004 (m) cc_final: 0.8650 (t) REVERT: C 87 GLN cc_start: 0.7936 (mt0) cc_final: 0.7603 (mt0) REVERT: C 237 LYS cc_start: 0.6873 (mtmt) cc_final: 0.6569 (mmtt) REVERT: C 248 ILE cc_start: 0.8048 (mt) cc_final: 0.7845 (mt) REVERT: C 250 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6996 (mt-10) REVERT: D 86 VAL cc_start: 0.8644 (p) cc_final: 0.8328 (t) REVERT: D 142 ILE cc_start: 0.8704 (mp) cc_final: 0.8298 (pt) REVERT: D 160 PRO cc_start: 0.8703 (Cg_endo) cc_final: 0.8442 (Cg_exo) REVERT: D 164 LYS cc_start: 0.7860 (pttp) cc_final: 0.7553 (ptmm) REVERT: D 198 LYS cc_start: 0.7140 (tptm) cc_final: 0.6938 (ttmt) REVERT: D 227 ASP cc_start: 0.6617 (t0) cc_final: 0.5914 (m-30) REVERT: D 237 LYS cc_start: 0.7054 (mtmm) cc_final: 0.6688 (mmtm) REVERT: D 240 LYS cc_start: 0.7981 (tttt) cc_final: 0.7769 (tttp) REVERT: D 250 GLU cc_start: 0.7252 (pt0) cc_final: 0.6838 (pt0) REVERT: D 276 ASP cc_start: 0.7306 (m-30) cc_final: 0.7017 (m-30) REVERT: E 46 LYS cc_start: 0.8088 (ptpp) cc_final: 0.7737 (mmmt) REVERT: E 56 ARG cc_start: 0.7709 (mtt90) cc_final: 0.7502 (mtt180) REVERT: E 155 THR cc_start: 0.8955 (t) cc_final: 0.8675 (m) REVERT: E 158 GLU cc_start: 0.7239 (pt0) cc_final: 0.5947 (tp30) REVERT: E 200 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6891 (mtt90) REVERT: E 237 LYS cc_start: 0.7569 (pttm) cc_final: 0.7082 (ptpp) REVERT: E 240 LYS cc_start: 0.7100 (ttpt) cc_final: 0.6833 (tttt) REVERT: E 250 GLU cc_start: 0.7151 (pt0) cc_final: 0.6865 (tt0) REVERT: E 287 GLU cc_start: 0.6616 (tt0) cc_final: 0.6392 (tt0) REVERT: F 31 GLU cc_start: 0.6591 (tp30) cc_final: 0.6096 (mp0) REVERT: F 87 GLN cc_start: 0.7880 (mt0) cc_final: 0.7595 (mt0) REVERT: F 106 SER cc_start: 0.8558 (p) cc_final: 0.8301 (m) REVERT: F 118 TYR cc_start: 0.7896 (p90) cc_final: 0.7291 (p90) REVERT: F 140 VAL cc_start: 0.8539 (t) cc_final: 0.8248 (p) REVERT: F 142 ILE cc_start: 0.8528 (mt) cc_final: 0.7936 (pt) REVERT: F 154 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8142 (mtpt) REVERT: F 188 ASN cc_start: 0.8083 (t0) cc_final: 0.7859 (t0) REVERT: F 198 LYS cc_start: 0.7467 (tttp) cc_final: 0.7256 (ttmt) REVERT: F 209 ASN cc_start: 0.8420 (t0) cc_final: 0.8116 (t0) REVERT: F 232 ILE cc_start: 0.8306 (pt) cc_final: 0.8060 (mt) REVERT: F 237 LYS cc_start: 0.6786 (mtmm) cc_final: 0.6555 (mmtt) REVERT: F 277 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.6939 (ttm170) REVERT: G 46 LYS cc_start: 0.8064 (pttm) cc_final: 0.7277 (mmmt) REVERT: G 111 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7514 (mt-10) REVERT: G 164 LYS cc_start: 0.8238 (ptmm) cc_final: 0.8035 (ptmm) REVERT: G 227 ASP cc_start: 0.6436 (t0) cc_final: 0.6038 (m-30) REVERT: G 237 LYS cc_start: 0.7943 (pttm) cc_final: 0.7241 (ttmt) REVERT: G 293 ASN cc_start: 0.7218 (p0) cc_final: 0.6912 (p0) outliers start: 9 outliers final: 4 residues processed: 678 average time/residue: 0.3729 time to fit residues: 353.0283 Evaluate side-chains 365 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 361 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain D residue 101 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 HIS B 194 GLN C 48 HIS C 293 ASN D 32 ASN E 259 HIS F 242 GLN F 293 ASN G 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.142005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.129755 restraints weight = 63581.834| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.36 r_work: 0.3308 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16789 Z= 0.099 Angle : 0.459 6.130 22729 Z= 0.244 Chirality : 0.044 0.171 2430 Planarity : 0.003 0.071 2935 Dihedral : 3.749 42.165 2229 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 1.32 % Allowed : 11.03 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -0.84 (0.19), residues: 2040 helix: -0.82 (0.74), residues: 42 sheet: -0.36 (0.16), residues: 1107 loop : -0.62 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 200 TYR 0.014 0.001 TYR D 68 PHE 0.013 0.001 PHE D 42 TRP 0.006 0.001 TRP G 286 HIS 0.003 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00222 (16789) covalent geometry : angle 0.45861 (22729) hydrogen bonds : bond 0.04546 ( 177) hydrogen bonds : angle 8.81032 ( 420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 396 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 372 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7924 (ptpp) cc_final: 0.7665 (pttp) REVERT: A 118 TYR cc_start: 0.7934 (p90) cc_final: 0.7455 (p90) REVERT: A 164 LYS cc_start: 0.8053 (tttm) cc_final: 0.7738 (tptp) REVERT: A 227 ASP cc_start: 0.6385 (t0) cc_final: 0.6074 (m-30) REVERT: B 227 ASP cc_start: 0.6726 (t0) cc_final: 0.6276 (m-30) REVERT: B 233 THR cc_start: 0.8519 (p) cc_final: 0.8284 (p) REVERT: C 21 LYS cc_start: 0.8271 (tppt) cc_final: 0.7997 (mmtt) REVERT: C 250 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7049 (mt-10) REVERT: D 142 ILE cc_start: 0.8849 (mp) cc_final: 0.8552 (pt) REVERT: D 160 PRO cc_start: 0.8776 (Cg_endo) cc_final: 0.8423 (Cg_exo) REVERT: D 227 ASP cc_start: 0.6269 (t0) cc_final: 0.5990 (m-30) REVERT: D 250 GLU cc_start: 0.7331 (pt0) cc_final: 0.6950 (pt0) REVERT: D 277 ARG cc_start: 0.7534 (mtp85) cc_final: 0.6790 (ttm-80) REVERT: D 281 ARG cc_start: 0.8749 (ttm170) cc_final: 0.8526 (ttm-80) REVERT: E 31 GLU cc_start: 0.6963 (mp0) cc_final: 0.6353 (mp0) REVERT: E 155 THR cc_start: 0.8992 (t) cc_final: 0.8703 (m) REVERT: E 158 GLU cc_start: 0.7309 (pt0) cc_final: 0.6667 (tp30) REVERT: E 200 ARG cc_start: 0.7425 (mtt180) cc_final: 0.7218 (mtt90) REVERT: E 237 LYS cc_start: 0.7774 (pttm) cc_final: 0.7471 (ptpp) REVERT: F 142 ILE cc_start: 0.8801 (mt) cc_final: 0.8435 (pt) REVERT: F 160 PRO cc_start: 0.8457 (Cg_endo) cc_final: 0.7978 (Cg_exo) REVERT: F 276 ASP cc_start: 0.7542 (p0) cc_final: 0.6823 (p0) REVERT: F 277 ARG cc_start: 0.7567 (mtp-110) cc_final: 0.7006 (ttm-80) REVERT: F 283 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7840 (ttmm) REVERT: G 29 ASP cc_start: 0.7423 (t0) cc_final: 0.6927 (t0) REVERT: G 46 LYS cc_start: 0.8332 (pttm) cc_final: 0.8013 (mmmt) REVERT: G 101 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7404 (p90) REVERT: G 111 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7500 (mt-10) REVERT: G 164 LYS cc_start: 0.8748 (ptmm) cc_final: 0.8544 (ptmm) REVERT: G 237 LYS cc_start: 0.7993 (pttm) cc_final: 0.7631 (ttmt) REVERT: G 293 ASN cc_start: 0.7542 (p0) cc_final: 0.7213 (p0) outliers start: 24 outliers final: 19 residues processed: 392 average time/residue: 0.3517 time to fit residues: 195.1339 Evaluate side-chains 342 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 322 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 201 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN C 32 ASN C 172 ASN D 48 HIS D 209 ASN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN G 35 HIS G 201 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.123231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.110442 restraints weight = 59355.949| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.32 r_work: 0.3108 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 16789 Z= 0.316 Angle : 0.648 5.373 22729 Z= 0.353 Chirality : 0.049 0.171 2430 Planarity : 0.005 0.063 2935 Dihedral : 5.048 36.526 2227 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.36 % Favored : 92.54 % Rotamer: Outliers : 2.81 % Allowed : 12.18 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -1.15 (0.18), residues: 2040 helix: -1.50 (0.67), residues: 42 sheet: -0.59 (0.16), residues: 1128 loop : -0.76 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 184 TYR 0.022 0.003 TYR F 28 PHE 0.035 0.003 PHE F 228 TRP 0.011 0.002 TRP G 274 HIS 0.015 0.003 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00764 (16789) covalent geometry : angle 0.64789 (22729) hydrogen bonds : bond 0.04427 ( 177) hydrogen bonds : angle 7.78191 ( 420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8089 (ptpp) cc_final: 0.7748 (pttp) REVERT: A 118 TYR cc_start: 0.8011 (p90) cc_final: 0.7340 (p90) REVERT: A 227 ASP cc_start: 0.6433 (t0) cc_final: 0.6128 (m-30) REVERT: A 277 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7365 (ttt180) REVERT: B 56 ARG cc_start: 0.8168 (mmt-90) cc_final: 0.7860 (mmt90) REVERT: B 147 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8294 (ttpp) REVERT: B 227 ASP cc_start: 0.6612 (t0) cc_final: 0.6173 (m-30) REVERT: B 237 LYS cc_start: 0.7980 (mmtm) cc_final: 0.7744 (mmtt) REVERT: C 21 LYS cc_start: 0.8567 (tppt) cc_final: 0.8329 (mmmm) REVERT: C 94 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6663 (mm-30) REVERT: C 142 ILE cc_start: 0.8799 (mt) cc_final: 0.8597 (pt) REVERT: C 183 ASP cc_start: 0.8161 (p0) cc_final: 0.7926 (p0) REVERT: D 142 ILE cc_start: 0.8894 (mp) cc_final: 0.8586 (pt) REVERT: D 290 GLU cc_start: 0.7974 (pt0) cc_final: 0.7679 (pt0) REVERT: E 200 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7559 (mtt90) REVERT: E 237 LYS cc_start: 0.8173 (pttm) cc_final: 0.7892 (ptpp) REVERT: F 31 GLU cc_start: 0.7118 (mp0) cc_final: 0.6789 (mp0) REVERT: F 75 LYS cc_start: 0.7754 (ttmm) cc_final: 0.7521 (ptpp) REVERT: F 142 ILE cc_start: 0.8758 (mt) cc_final: 0.8354 (pt) REVERT: F 227 ASP cc_start: 0.6709 (t0) cc_final: 0.6300 (m-30) REVERT: F 276 ASP cc_start: 0.8099 (p0) cc_final: 0.7096 (p0) REVERT: F 277 ARG cc_start: 0.7796 (mtp-110) cc_final: 0.7568 (ptm-80) REVERT: F 283 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7880 (ttmt) REVERT: G 237 LYS cc_start: 0.8186 (pttm) cc_final: 0.7627 (ttmt) outliers start: 51 outliers final: 44 residues processed: 360 average time/residue: 0.3322 time to fit residues: 173.8346 Evaluate side-chains 327 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 201 ASN Chi-restraints excluded: chain G residue 292 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 178 ASN C 173 ASN C 178 ASN C 293 ASN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.123609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.110227 restraints weight = 66563.039| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.43 r_work: 0.3094 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16789 Z= 0.167 Angle : 0.512 4.547 22729 Z= 0.275 Chirality : 0.045 0.145 2430 Planarity : 0.004 0.058 2935 Dihedral : 4.646 37.501 2227 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.94 % Favored : 94.01 % Rotamer: Outliers : 2.81 % Allowed : 13.12 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -1.15 (0.18), residues: 2040 helix: -1.63 (0.70), residues: 42 sheet: -0.47 (0.16), residues: 1107 loop : -0.94 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 104 TYR 0.016 0.002 TYR F 249 PHE 0.016 0.002 PHE F 228 TRP 0.007 0.001 TRP D 274 HIS 0.006 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00396 (16789) covalent geometry : angle 0.51185 (22729) hydrogen bonds : bond 0.03317 ( 177) hydrogen bonds : angle 7.18093 ( 420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7794 (pttp) REVERT: A 118 TYR cc_start: 0.8015 (p90) cc_final: 0.7314 (p90) REVERT: A 227 ASP cc_start: 0.6363 (t0) cc_final: 0.6106 (m-30) REVERT: A 277 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7342 (ttt180) REVERT: B 56 ARG cc_start: 0.8162 (mmt-90) cc_final: 0.7901 (mmt90) REVERT: B 147 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8265 (ttpp) REVERT: B 227 ASP cc_start: 0.6547 (t0) cc_final: 0.6157 (m-30) REVERT: B 237 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7736 (mmtt) REVERT: C 94 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6805 (mm-30) REVERT: C 253 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7896 (mpp80) REVERT: D 142 ILE cc_start: 0.8862 (mp) cc_final: 0.8554 (pt) REVERT: D 237 LYS cc_start: 0.7987 (mmtm) cc_final: 0.7761 (mmtt) REVERT: D 250 GLU cc_start: 0.7637 (tt0) cc_final: 0.7402 (tt0) REVERT: D 290 GLU cc_start: 0.7970 (pt0) cc_final: 0.7670 (pt0) REVERT: E 31 GLU cc_start: 0.7404 (mp0) cc_final: 0.6835 (mp0) REVERT: E 200 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7595 (mtt90) REVERT: E 237 LYS cc_start: 0.8235 (pttm) cc_final: 0.7854 (ptpp) REVERT: F 31 GLU cc_start: 0.7210 (mp0) cc_final: 0.6962 (mp0) REVERT: F 142 ILE cc_start: 0.8769 (mt) cc_final: 0.8430 (pt) REVERT: F 227 ASP cc_start: 0.6685 (t0) cc_final: 0.6239 (m-30) REVERT: F 277 ARG cc_start: 0.7751 (mtp-110) cc_final: 0.7503 (ptm160) REVERT: F 283 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7795 (ttmm) REVERT: G 75 LYS cc_start: 0.7868 (pttm) cc_final: 0.7539 (pttm) REVERT: G 237 LYS cc_start: 0.8273 (pttm) cc_final: 0.7678 (ttmt) outliers start: 51 outliers final: 42 residues processed: 330 average time/residue: 0.3225 time to fit residues: 156.5021 Evaluate side-chains 327 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 161 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 25 optimal weight: 0.0770 chunk 121 optimal weight: 2.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.124932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.112010 restraints weight = 60604.102| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.35 r_work: 0.3103 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16789 Z= 0.107 Angle : 0.458 4.332 22729 Z= 0.243 Chirality : 0.044 0.140 2430 Planarity : 0.003 0.054 2935 Dihedral : 4.287 37.737 2227 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 1.98 % Allowed : 14.44 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -1.26 (0.18), residues: 2040 helix: -2.88 (0.43), residues: 77 sheet: -0.49 (0.15), residues: 1142 loop : -0.93 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 184 TYR 0.013 0.001 TYR F 249 PHE 0.010 0.001 PHE F 228 TRP 0.006 0.001 TRP D 274 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00254 (16789) covalent geometry : angle 0.45769 (22729) hydrogen bonds : bond 0.02855 ( 177) hydrogen bonds : angle 6.72495 ( 420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7792 (pttp) REVERT: A 118 TYR cc_start: 0.7933 (p90) cc_final: 0.7257 (p90) REVERT: A 121 ASN cc_start: 0.8099 (p0) cc_final: 0.7895 (p0) REVERT: A 227 ASP cc_start: 0.6357 (t0) cc_final: 0.6075 (m-30) REVERT: A 277 ARG cc_start: 0.7652 (ttm170) cc_final: 0.7272 (ttt180) REVERT: B 56 ARG cc_start: 0.8045 (mmt-90) cc_final: 0.7762 (mmt90) REVERT: B 147 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8236 (ttpp) REVERT: B 227 ASP cc_start: 0.6536 (t0) cc_final: 0.6158 (m-30) REVERT: B 237 LYS cc_start: 0.7892 (mmtm) cc_final: 0.7659 (mmtt) REVERT: C 253 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7545 (mpp80) REVERT: D 141 SER cc_start: 0.8850 (m) cc_final: 0.8508 (t) REVERT: D 142 ILE cc_start: 0.8813 (mp) cc_final: 0.8473 (pt) REVERT: D 237 LYS cc_start: 0.7995 (mmtm) cc_final: 0.7776 (mmtt) REVERT: D 250 GLU cc_start: 0.7572 (tt0) cc_final: 0.7333 (tt0) REVERT: D 290 GLU cc_start: 0.7931 (pt0) cc_final: 0.7648 (pt0) REVERT: E 31 GLU cc_start: 0.7325 (mp0) cc_final: 0.6776 (mp0) REVERT: E 200 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7608 (mtt90) REVERT: E 237 LYS cc_start: 0.8116 (pttm) cc_final: 0.7745 (ptpp) REVERT: E 290 GLU cc_start: 0.7834 (pt0) cc_final: 0.7552 (pt0) REVERT: F 31 GLU cc_start: 0.7255 (mp0) cc_final: 0.6992 (mp0) REVERT: F 142 ILE cc_start: 0.8757 (mt) cc_final: 0.8452 (pt) REVERT: F 227 ASP cc_start: 0.6664 (t0) cc_final: 0.6268 (m-30) REVERT: F 231 VAL cc_start: 0.8842 (p) cc_final: 0.8586 (t) REVERT: F 277 ARG cc_start: 0.7749 (mtp-110) cc_final: 0.7518 (ptm160) REVERT: F 283 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7767 (ttmm) REVERT: G 75 LYS cc_start: 0.7874 (pttm) cc_final: 0.7485 (pttm) REVERT: G 237 LYS cc_start: 0.8233 (pttm) cc_final: 0.7636 (ttmt) outliers start: 36 outliers final: 32 residues processed: 316 average time/residue: 0.3337 time to fit residues: 153.8578 Evaluate side-chains 316 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 161 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 142 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 26 optimal weight: 0.0670 chunk 190 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN B 201 ASN B 293 ASN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.123298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.110106 restraints weight = 64216.317| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.39 r_work: 0.3069 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16789 Z= 0.133 Angle : 0.472 4.378 22729 Z= 0.251 Chirality : 0.044 0.138 2430 Planarity : 0.003 0.051 2935 Dihedral : 4.338 37.531 2227 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.37 % Rotamer: Outliers : 2.81 % Allowed : 14.17 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -1.29 (0.18), residues: 2040 helix: -2.94 (0.42), residues: 77 sheet: -0.51 (0.15), residues: 1142 loop : -0.95 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 184 TYR 0.014 0.001 TYR F 249 PHE 0.013 0.001 PHE D 228 TRP 0.006 0.001 TRP D 179 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00320 (16789) covalent geometry : angle 0.47201 (22729) hydrogen bonds : bond 0.02877 ( 177) hydrogen bonds : angle 6.54758 ( 420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8131 (ptpp) cc_final: 0.7823 (pttp) REVERT: A 86 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8587 (p) REVERT: A 142 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8668 (pt) REVERT: A 227 ASP cc_start: 0.6420 (t0) cc_final: 0.6196 (m-30) REVERT: A 277 ARG cc_start: 0.7699 (ttm170) cc_final: 0.7331 (ttt180) REVERT: B 56 ARG cc_start: 0.8068 (mmt-90) cc_final: 0.7737 (mmt180) REVERT: B 147 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8270 (ttpp) REVERT: B 227 ASP cc_start: 0.6563 (t0) cc_final: 0.6162 (m-30) REVERT: B 237 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7690 (mmtt) REVERT: B 276 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7801 (p0) REVERT: C 253 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7839 (mpp80) REVERT: D 142 ILE cc_start: 0.8802 (mp) cc_final: 0.8470 (pt) REVERT: D 237 LYS cc_start: 0.8019 (mmtm) cc_final: 0.7805 (mmtt) REVERT: D 250 GLU cc_start: 0.7629 (tt0) cc_final: 0.7358 (tt0) REVERT: D 290 GLU cc_start: 0.7913 (pt0) cc_final: 0.7634 (pt0) REVERT: E 237 LYS cc_start: 0.8187 (pttm) cc_final: 0.7810 (ptpp) REVERT: E 290 GLU cc_start: 0.7872 (pt0) cc_final: 0.7573 (pt0) REVERT: F 31 GLU cc_start: 0.7278 (mp0) cc_final: 0.7039 (mp0) REVERT: F 46 LYS cc_start: 0.8465 (pttp) cc_final: 0.8129 (mmmt) REVERT: F 142 ILE cc_start: 0.8747 (mt) cc_final: 0.8463 (pt) REVERT: F 227 ASP cc_start: 0.6754 (t0) cc_final: 0.6375 (m-30) REVERT: F 231 VAL cc_start: 0.8806 (p) cc_final: 0.8594 (t) REVERT: F 251 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8645 (ptp90) REVERT: F 277 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7516 (ptm160) REVERT: F 283 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7769 (ttmm) REVERT: G 68 TYR cc_start: 0.8598 (p90) cc_final: 0.8383 (p90) REVERT: G 237 LYS cc_start: 0.8273 (pttm) cc_final: 0.7645 (ttmt) outliers start: 51 outliers final: 38 residues processed: 313 average time/residue: 0.3271 time to fit residues: 149.5164 Evaluate side-chains 316 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 161 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 172 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 ASN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.121669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.108773 restraints weight = 60952.650| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.34 r_work: 0.3055 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16789 Z= 0.181 Angle : 0.501 4.554 22729 Z= 0.268 Chirality : 0.045 0.139 2430 Planarity : 0.004 0.048 2935 Dihedral : 4.533 37.323 2227 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.17 % Favored : 92.78 % Rotamer: Outliers : 2.92 % Allowed : 14.77 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -1.40 (0.18), residues: 2040 helix: -3.09 (0.40), residues: 77 sheet: -0.61 (0.15), residues: 1149 loop : -0.97 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 184 TYR 0.015 0.002 TYR F 249 PHE 0.016 0.002 PHE D 228 TRP 0.005 0.001 TRP D 274 HIS 0.006 0.002 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00434 (16789) covalent geometry : angle 0.50088 (22729) hydrogen bonds : bond 0.03021 ( 177) hydrogen bonds : angle 6.57072 ( 420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8168 (ptpp) cc_final: 0.7879 (pttp) REVERT: A 86 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8605 (p) REVERT: A 118 TYR cc_start: 0.8072 (p90) cc_final: 0.7349 (p90) REVERT: A 142 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8683 (pt) REVERT: A 227 ASP cc_start: 0.6420 (t0) cc_final: 0.6203 (m-30) REVERT: A 275 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8229 (t) REVERT: A 277 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7333 (ttt180) REVERT: B 56 ARG cc_start: 0.8054 (mmt-90) cc_final: 0.7835 (mmt180) REVERT: B 147 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8304 (ttpp) REVERT: B 227 ASP cc_start: 0.6594 (t0) cc_final: 0.6223 (m-30) REVERT: B 237 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7674 (mmtt) REVERT: B 276 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7854 (p0) REVERT: C 253 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7911 (mpp80) REVERT: D 142 ILE cc_start: 0.8818 (mp) cc_final: 0.8488 (pt) REVERT: D 290 GLU cc_start: 0.7910 (pt0) cc_final: 0.7622 (pt0) REVERT: E 86 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8525 (p) REVERT: E 237 LYS cc_start: 0.8217 (pttm) cc_final: 0.7861 (ptpp) REVERT: E 290 GLU cc_start: 0.7874 (pt0) cc_final: 0.7569 (pt0) REVERT: F 31 GLU cc_start: 0.7301 (mp0) cc_final: 0.7083 (mp0) REVERT: F 46 LYS cc_start: 0.8478 (pttp) cc_final: 0.8150 (mmmt) REVERT: F 142 ILE cc_start: 0.8764 (mt) cc_final: 0.8489 (pt) REVERT: F 227 ASP cc_start: 0.6793 (t0) cc_final: 0.6399 (m-30) REVERT: F 231 VAL cc_start: 0.8838 (p) cc_final: 0.8636 (t) REVERT: F 251 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8656 (ptp90) REVERT: F 277 ARG cc_start: 0.7786 (mtp-110) cc_final: 0.7509 (ptm160) REVERT: F 283 LYS cc_start: 0.8012 (ttpt) cc_final: 0.7788 (ttmm) REVERT: G 237 LYS cc_start: 0.8307 (pttm) cc_final: 0.7726 (ttmt) outliers start: 53 outliers final: 42 residues processed: 312 average time/residue: 0.3259 time to fit residues: 148.6606 Evaluate side-chains 326 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 292 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 137 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN B 201 ASN B 293 ASN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.121507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.108543 restraints weight = 63176.382| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.36 r_work: 0.3045 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16789 Z= 0.156 Angle : 0.487 4.760 22729 Z= 0.260 Chirality : 0.044 0.139 2430 Planarity : 0.003 0.050 2935 Dihedral : 4.513 36.942 2227 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.73 % Favored : 93.23 % Rotamer: Outliers : 2.81 % Allowed : 14.83 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -1.44 (0.18), residues: 2040 helix: -3.19 (0.39), residues: 77 sheet: -0.64 (0.15), residues: 1149 loop : -0.97 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 184 TYR 0.013 0.001 TYR F 249 PHE 0.013 0.001 PHE D 228 TRP 0.006 0.001 TRP D 274 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00373 (16789) covalent geometry : angle 0.48722 (22729) hydrogen bonds : bond 0.02944 ( 177) hydrogen bonds : angle 6.49090 ( 420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 330 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8167 (ptpp) cc_final: 0.7866 (pttp) REVERT: A 86 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8568 (p) REVERT: A 142 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8699 (pt) REVERT: A 227 ASP cc_start: 0.6440 (t0) cc_final: 0.6193 (m-30) REVERT: A 275 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8217 (t) REVERT: A 277 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7343 (ttt180) REVERT: B 56 ARG cc_start: 0.8041 (mmt-90) cc_final: 0.7839 (mmt180) REVERT: B 147 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8301 (ttpp) REVERT: B 227 ASP cc_start: 0.6588 (t0) cc_final: 0.6228 (m-30) REVERT: B 237 LYS cc_start: 0.7922 (mmtm) cc_final: 0.7680 (mmtt) REVERT: B 276 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7732 (p0) REVERT: C 253 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7890 (mpp80) REVERT: D 142 ILE cc_start: 0.8827 (mp) cc_final: 0.8482 (pt) REVERT: D 290 GLU cc_start: 0.7868 (pt0) cc_final: 0.7573 (pt0) REVERT: E 86 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8504 (p) REVERT: E 237 LYS cc_start: 0.8184 (pttm) cc_final: 0.7818 (ptpp) REVERT: E 290 GLU cc_start: 0.7853 (pt0) cc_final: 0.7545 (pt0) REVERT: F 31 GLU cc_start: 0.7313 (mp0) cc_final: 0.7099 (mp0) REVERT: F 46 LYS cc_start: 0.8460 (pttp) cc_final: 0.8123 (mmmt) REVERT: F 142 ILE cc_start: 0.8806 (mt) cc_final: 0.8517 (pt) REVERT: F 227 ASP cc_start: 0.6773 (t0) cc_final: 0.6408 (m-30) REVERT: F 251 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8629 (ptp90) REVERT: F 277 ARG cc_start: 0.7807 (mtp-110) cc_final: 0.7557 (ptm160) REVERT: F 283 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7775 (ttmm) REVERT: G 68 TYR cc_start: 0.8628 (p90) cc_final: 0.8405 (p90) REVERT: G 108 ASP cc_start: 0.7773 (m-30) cc_final: 0.7519 (m-30) REVERT: G 215 LYS cc_start: 0.8897 (mttp) cc_final: 0.8601 (mttt) REVERT: G 237 LYS cc_start: 0.8292 (pttm) cc_final: 0.7674 (ttmt) outliers start: 51 outliers final: 41 residues processed: 312 average time/residue: 0.3334 time to fit residues: 151.6486 Evaluate side-chains 321 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 292 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 95 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS B 201 ASN ** D 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.120703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.107714 restraints weight = 61789.919| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.36 r_work: 0.3038 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 16789 Z= 0.193 Angle : 0.511 5.012 22729 Z= 0.275 Chirality : 0.045 0.139 2430 Planarity : 0.004 0.049 2935 Dihedral : 4.654 36.842 2227 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.46 % Favored : 92.49 % Rotamer: Outliers : 2.65 % Allowed : 15.10 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -1.50 (0.18), residues: 2040 helix: -3.32 (0.37), residues: 77 sheet: -0.68 (0.15), residues: 1149 loop : -1.01 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 200 TYR 0.015 0.002 TYR F 249 PHE 0.016 0.002 PHE D 228 TRP 0.005 0.001 TRP B 179 HIS 0.006 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00462 (16789) covalent geometry : angle 0.51117 (22729) hydrogen bonds : bond 0.03049 ( 177) hydrogen bonds : angle 6.52858 ( 420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8167 (ptpp) cc_final: 0.7854 (pttp) REVERT: A 68 TYR cc_start: 0.8731 (p90) cc_final: 0.8399 (p90) REVERT: A 86 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8595 (p) REVERT: A 227 ASP cc_start: 0.6464 (t0) cc_final: 0.6225 (m-30) REVERT: A 275 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8229 (t) REVERT: A 277 ARG cc_start: 0.7749 (ttm170) cc_final: 0.7372 (ttt180) REVERT: B 147 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8324 (ttpp) REVERT: B 227 ASP cc_start: 0.6638 (t0) cc_final: 0.6234 (m-30) REVERT: B 276 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7788 (p0) REVERT: B 290 GLU cc_start: 0.7863 (pt0) cc_final: 0.7467 (pt0) REVERT: B 293 ASN cc_start: 0.7310 (t0) cc_final: 0.7028 (t0) REVERT: C 147 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8145 (ttpp) REVERT: C 253 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7959 (mpp80) REVERT: D 142 ILE cc_start: 0.8840 (mp) cc_final: 0.8499 (pt) REVERT: D 290 GLU cc_start: 0.7881 (pt0) cc_final: 0.7583 (pt0) REVERT: E 86 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8525 (p) REVERT: E 178 ASN cc_start: 0.8026 (m-40) cc_final: 0.7811 (m-40) REVERT: E 237 LYS cc_start: 0.8202 (pttm) cc_final: 0.7812 (ptpp) REVERT: E 290 GLU cc_start: 0.7902 (pt0) cc_final: 0.7634 (pt0) REVERT: F 46 LYS cc_start: 0.8496 (pttp) cc_final: 0.8131 (mmmt) REVERT: F 142 ILE cc_start: 0.8822 (mt) cc_final: 0.8521 (pt) REVERT: F 227 ASP cc_start: 0.6773 (t0) cc_final: 0.6434 (m-30) REVERT: F 251 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8643 (ptp90) REVERT: F 277 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7533 (ptm160) REVERT: F 283 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7815 (ttmm) REVERT: G 68 TYR cc_start: 0.8670 (p90) cc_final: 0.8429 (p90) REVERT: G 108 ASP cc_start: 0.7853 (m-30) cc_final: 0.7639 (m-30) REVERT: G 215 LYS cc_start: 0.8868 (mttp) cc_final: 0.8576 (mttt) REVERT: G 237 LYS cc_start: 0.8271 (pttm) cc_final: 0.7602 (ttmt) outliers start: 48 outliers final: 40 residues processed: 315 average time/residue: 0.2910 time to fit residues: 133.8027 Evaluate side-chains 322 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 165 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 196 optimal weight: 0.0980 chunk 149 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN B 105 ASN D 144 HIS ** D 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.123433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110233 restraints weight = 65979.723| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.42 r_work: 0.3064 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16789 Z= 0.086 Angle : 0.446 4.253 22729 Z= 0.236 Chirality : 0.043 0.140 2430 Planarity : 0.003 0.048 2935 Dihedral : 4.285 37.530 2227 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 1.82 % Allowed : 15.88 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -1.33 (0.19), residues: 2040 helix: -3.22 (0.39), residues: 77 sheet: -0.61 (0.16), residues: 1142 loop : -0.80 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 277 TYR 0.010 0.001 TYR F 249 PHE 0.007 0.001 PHE C 39 TRP 0.007 0.001 TRP B 167 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00204 (16789) covalent geometry : angle 0.44621 (22729) hydrogen bonds : bond 0.02558 ( 177) hydrogen bonds : angle 6.26480 ( 420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Evaluate side-chains 312 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8108 (ptpp) cc_final: 0.7810 (pttp) REVERT: A 121 ASN cc_start: 0.8088 (p0) cc_final: 0.7810 (p0) REVERT: A 227 ASP cc_start: 0.6388 (t0) cc_final: 0.6130 (m-30) REVERT: A 277 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7294 (ttt180) REVERT: B 147 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8256 (ttpp) REVERT: B 227 ASP cc_start: 0.6597 (t0) cc_final: 0.6263 (m-30) REVERT: B 276 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7652 (p0) REVERT: C 253 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7637 (mpp80) REVERT: D 141 SER cc_start: 0.8798 (m) cc_final: 0.8505 (t) REVERT: D 142 ILE cc_start: 0.8829 (mp) cc_final: 0.8473 (pt) REVERT: D 290 GLU cc_start: 0.7890 (pt0) cc_final: 0.7594 (pt0) REVERT: E 86 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8430 (p) REVERT: E 87 GLN cc_start: 0.8270 (pt0) cc_final: 0.7944 (pt0) REVERT: E 237 LYS cc_start: 0.8125 (pttm) cc_final: 0.7777 (ptpp) REVERT: E 290 GLU cc_start: 0.7857 (pt0) cc_final: 0.7557 (pt0) REVERT: F 46 LYS cc_start: 0.8447 (pttp) cc_final: 0.8079 (mmmt) REVERT: F 142 ILE cc_start: 0.8765 (mt) cc_final: 0.8474 (pt) REVERT: F 227 ASP cc_start: 0.6704 (t0) cc_final: 0.6412 (m-30) REVERT: F 283 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7774 (ttmm) REVERT: G 108 ASP cc_start: 0.7739 (m-30) cc_final: 0.7524 (m-30) REVERT: G 215 LYS cc_start: 0.8898 (mttp) cc_final: 0.8592 (mttt) REVERT: G 237 LYS cc_start: 0.8310 (pttm) cc_final: 0.7671 (ttmt) outliers start: 33 outliers final: 27 residues processed: 298 average time/residue: 0.3393 time to fit residues: 147.5125 Evaluate side-chains 304 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 161 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 201 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 178 ASN B 293 ASN ** D 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.120764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.107475 restraints weight = 67151.561| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.42 r_work: 0.3027 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16789 Z= 0.172 Angle : 0.497 4.888 22729 Z= 0.265 Chirality : 0.045 0.141 2430 Planarity : 0.004 0.046 2935 Dihedral : 4.505 36.714 2227 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.85 % Favored : 92.10 % Rotamer: Outliers : 1.87 % Allowed : 15.82 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % 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 aren not related in a simple way. whole: -1.42 (0.18), residues: 2040 helix: -3.30 (0.38), residues: 77 sheet: -0.66 (0.15), residues: 1142 loop : -0.90 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 104 TYR 0.014 0.002 TYR F 249 PHE 0.015 0.002 PHE D 228 TRP 0.005 0.001 TRP B 179 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00410 (16789) covalent geometry : angle 0.49690 (22729) hydrogen bonds : bond 0.02906 ( 177) hydrogen bonds : angle 6.36458 ( 420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8771.82 seconds wall clock time: 149 minutes 45.54 seconds (8985.54 seconds total)