Starting phenix.real_space_refine on Sun Aug 24 01:02:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8edx_28042/08_2025/8edx_28042.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edx_28042/08_2025/8edx_28042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8edx_28042/08_2025/8edx_28042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edx_28042/08_2025/8edx_28042.map" model { file = "/net/cci-nas-00/data/ceres_data/8edx_28042/08_2025/8edx_28042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edx_28042/08_2025/8edx_28042.cif" } resolution = 2.81 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= 0.007 sd= 0.192 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 10242 2.51 5 N 2724 2.21 5 O 3072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 16074 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "C" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "D" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "E" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "F" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Time building chain proxies: 2.96, per 1000 atoms: 0.18 Number of scatterers: 16074 At special positions: 0 Unit cell: (113.1, 121.8, 103.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 3072 8.00 N 2724 7.00 C 10242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 510.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3804 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 9.5% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 77 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 77 through 89 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 77 through 89 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 273 through 281 Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 77 through 89 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 273 through 281 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 57 through 59 No H-bonds generated for 'chain 'E' and resid 57 through 59' Processing helix chain 'E' and resid 77 through 89 Proline residue: E 86 - end of helix Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 273 through 281 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 77 through 89 Proline residue: F 86 - end of helix Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 273 through 281 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 12 removed outlier: 4.182A pdb=" N LEU A 8 " --> pdb=" O LEU A 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 30 through 31 current: chain 'A' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 61 through 75 current: chain 'A' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 104 through 107 current: chain 'A' and resid 131 through 146 removed outlier: 6.453A pdb=" N ASP A 157 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 142 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN A 155 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A 144 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 153 " --> pdb=" O PHE A 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 153 through 160 current: chain 'A' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 207 through 209 current: chain 'A' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 243 through 251 current: chain 'A' and resid 303 through 315 Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.831A pdb=" N ASP A 238 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 7 through 12 removed outlier: 4.182A pdb=" N LEU B 8 " --> pdb=" O LEU B 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 31 current: chain 'B' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 75 current: chain 'B' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 104 through 107 current: chain 'B' and resid 131 through 146 removed outlier: 6.453A pdb=" N ASP B 157 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B 142 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN B 155 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE B 144 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN B 153 " --> pdb=" O PHE B 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 153 through 160 current: chain 'B' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 207 through 209 current: chain 'B' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 243 through 251 current: chain 'B' and resid 303 through 315 Processing sheet with id=AA4, first strand: chain 'B' and resid 222 through 223 removed outlier: 3.831A pdb=" N ASP B 238 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 7 through 12 removed outlier: 4.183A pdb=" N LEU C 8 " --> pdb=" O LEU C 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 30 through 31 current: chain 'C' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 61 through 75 current: chain 'C' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 104 through 107 current: chain 'C' and resid 131 through 146 removed outlier: 6.452A pdb=" N ASP C 157 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 142 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN C 155 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE C 144 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN C 153 " --> pdb=" O PHE C 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 153 through 160 current: chain 'C' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 207 through 209 current: chain 'C' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 243 through 251 current: chain 'C' and resid 303 through 315 Processing sheet with id=AA6, first strand: chain 'C' and resid 222 through 223 removed outlier: 3.831A pdb=" N ASP C 238 " --> pdb=" O ASN C 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 7 through 12 removed outlier: 4.182A pdb=" N LEU D 8 " --> pdb=" O LEU D 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 30 through 31 current: chain 'D' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 61 through 75 current: chain 'D' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 104 through 107 current: chain 'D' and resid 131 through 146 removed outlier: 6.453A pdb=" N ASP D 157 " --> pdb=" O ASN D 140 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA D 142 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN D 155 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE D 144 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN D 153 " --> pdb=" O PHE D 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 153 through 160 current: chain 'D' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 207 through 209 current: chain 'D' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 243 through 251 current: chain 'D' and resid 303 through 315 Processing sheet with id=AA8, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.831A pdb=" N ASP D 238 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 7 through 12 removed outlier: 4.183A pdb=" N LEU E 8 " --> pdb=" O LEU E 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 31 current: chain 'E' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 61 through 75 current: chain 'E' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 104 through 107 current: chain 'E' and resid 131 through 146 removed outlier: 6.453A pdb=" N ASP E 157 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA E 142 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN E 155 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE E 144 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN E 153 " --> pdb=" O PHE E 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 153 through 160 current: chain 'E' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 207 through 209 current: chain 'E' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 243 through 251 current: chain 'E' and resid 303 through 315 Processing sheet with id=AB1, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.830A pdb=" N ASP E 238 " --> pdb=" O ASN E 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 7 through 12 removed outlier: 4.183A pdb=" N LEU F 8 " --> pdb=" O LEU F 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 30 through 31 current: chain 'F' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 61 through 75 current: chain 'F' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 104 through 107 current: chain 'F' and resid 131 through 146 removed outlier: 6.453A pdb=" N ASP F 157 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA F 142 " --> pdb=" O ASN F 155 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN F 155 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE F 144 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN F 153 " --> pdb=" O PHE F 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 153 through 160 current: chain 'F' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 207 through 209 current: chain 'F' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 243 through 251 current: chain 'F' and resid 303 through 315 Processing sheet with id=AB3, first strand: chain 'F' and resid 222 through 223 removed outlier: 3.831A pdb=" N ASP F 238 " --> pdb=" O ASN F 223 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2884 1.32 - 1.44: 4233 1.44 - 1.56: 9237 1.56 - 1.68: 2 1.68 - 1.80: 66 Bond restraints: 16422 Sorted by residual: bond pdb=" C LEU C 229 " pdb=" O LEU C 229 " ideal model delta sigma weight residual 1.236 1.201 0.036 1.16e-02 7.43e+03 9.39e+00 bond pdb=" C LEU A 229 " pdb=" O LEU A 229 " ideal model delta sigma weight residual 1.236 1.202 0.035 1.16e-02 7.43e+03 9.07e+00 bond pdb=" C LEU B 229 " pdb=" O LEU B 229 " ideal model delta sigma weight residual 1.236 1.202 0.035 1.16e-02 7.43e+03 8.91e+00 bond pdb=" C ARG B 56 " pdb=" O ARG B 56 " ideal model delta sigma weight residual 1.235 1.203 0.033 1.21e-02 6.83e+03 7.22e+00 bond pdb=" C ARG A 56 " pdb=" O ARG A 56 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.21e-02 6.83e+03 7.13e+00 ... (remaining 16417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 21263 1.23 - 2.47: 835 2.47 - 3.70: 177 3.70 - 4.94: 48 4.94 - 6.17: 3 Bond angle restraints: 22326 Sorted by residual: angle pdb=" N ASP D 251 " pdb=" CA ASP D 251 " pdb=" CB ASP D 251 " ideal model delta sigma weight residual 110.42 116.59 -6.17 1.52e+00 4.33e-01 1.65e+01 angle pdb=" N ASP F 251 " pdb=" CA ASP F 251 " pdb=" CB ASP F 251 " ideal model delta sigma weight residual 110.42 116.50 -6.08 1.52e+00 4.33e-01 1.60e+01 angle pdb=" CA LEU A 229 " pdb=" C LEU A 229 " pdb=" O LEU A 229 " ideal model delta sigma weight residual 120.90 116.95 3.95 1.03e+00 9.43e-01 1.47e+01 angle pdb=" CA LEU C 229 " pdb=" C LEU C 229 " pdb=" O LEU C 229 " ideal model delta sigma weight residual 120.90 116.96 3.94 1.03e+00 9.43e-01 1.47e+01 angle pdb=" CA LEU B 229 " pdb=" C LEU B 229 " pdb=" O LEU B 229 " ideal model delta sigma weight residual 120.90 117.06 3.84 1.03e+00 9.43e-01 1.39e+01 ... (remaining 22321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8837 17.07 - 34.14: 580 34.14 - 51.20: 205 51.20 - 68.27: 62 68.27 - 85.34: 48 Dihedral angle restraints: 9732 sinusoidal: 3774 harmonic: 5958 Sorted by residual: dihedral pdb=" CA ASP D 98 " pdb=" CB ASP D 98 " pdb=" CG ASP D 98 " pdb=" OD1 ASP D 98 " ideal model delta sinusoidal sigma weight residual -30.00 -86.43 56.43 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP A 98 " pdb=" CB ASP A 98 " pdb=" CG ASP A 98 " pdb=" OD1 ASP A 98 " ideal model delta sinusoidal sigma weight residual -30.00 -86.39 56.39 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP F 98 " pdb=" CB ASP F 98 " pdb=" CG ASP F 98 " pdb=" OD1 ASP F 98 " ideal model delta sinusoidal sigma weight residual -30.00 -86.38 56.38 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 9729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1486 0.035 - 0.070: 734 0.070 - 0.106: 209 0.106 - 0.141: 88 0.141 - 0.176: 3 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA LEU A 229 " pdb=" N LEU A 229 " pdb=" C LEU A 229 " pdb=" CB LEU A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA LEU C 229 " pdb=" N LEU C 229 " pdb=" C LEU C 229 " pdb=" CB LEU C 229 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA LEU B 229 " pdb=" N LEU B 229 " pdb=" C LEU B 229 " pdb=" CB LEU B 229 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 2517 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 56 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C ARG F 56 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG F 56 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN F 57 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 56 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ARG E 56 " -0.067 2.00e-02 2.50e+03 pdb=" O ARG E 56 " 0.025 2.00e-02 2.50e+03 pdb=" N GLN E 57 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 56 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C ARG D 56 " 0.066 2.00e-02 2.50e+03 pdb=" O ARG D 56 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN D 57 " -0.022 2.00e-02 2.50e+03 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 6340 2.88 - 3.39: 13946 3.39 - 3.89: 28071 3.89 - 4.40: 34531 4.40 - 4.90: 57984 Nonbonded interactions: 140872 Sorted by model distance: nonbonded pdb=" OE1 GLN E 57 " pdb=" OE1 GLU F 338 " model vdw 2.378 3.040 nonbonded pdb=" OE1 GLN D 57 " pdb=" OE1 GLU E 338 " model vdw 2.389 3.040 nonbonded pdb=" OE1 GLN B 57 " pdb=" OE1 GLU C 338 " model vdw 2.391 3.040 nonbonded pdb=" OE1 GLU D 338 " pdb=" OE1 GLN F 57 " model vdw 2.392 3.040 nonbonded pdb=" OE1 GLN A 57 " pdb=" OE1 GLU B 338 " model vdw 2.393 3.040 ... (remaining 140867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 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 : 0.006 0.042 16422 Z= 0.269 Angle : 0.598 6.172 22326 Z= 0.332 Chirality : 0.046 0.176 2520 Planarity : 0.005 0.045 2952 Dihedral : 15.442 85.340 5928 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.71 % Allowed : 16.19 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.15), residues: 2076 helix: -2.95 (0.40), residues: 120 sheet: -1.57 (0.15), residues: 900 loop : -2.01 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 56 TYR 0.014 0.002 TYR E 337 PHE 0.014 0.002 PHE F 214 TRP 0.002 0.001 TRP B 173 HIS 0.003 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00589 (16422) covalent geometry : angle 0.59773 (22326) hydrogen bonds : bond 0.19009 ( 120) hydrogen bonds : angle 6.51844 ( 324) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: D 46 GLN cc_start: 0.8358 (tp40) cc_final: 0.8092 (tp40) REVERT: D 48 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7601 (ppt170) REVERT: E 48 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7600 (ppt170) REVERT: E 164 ASP cc_start: 0.8429 (p0) cc_final: 0.8185 (p0) REVERT: F 48 ARG cc_start: 0.8123 (mtm180) cc_final: 0.7443 (ppt170) outliers start: 12 outliers final: 5 residues processed: 167 average time/residue: 0.7371 time to fit residues: 132.9459 Evaluate side-chains 129 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain F residue 251 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.0470 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 78 ASN A 309 HIS B 63 ASN B 78 ASN B 309 HIS C 63 ASN C 78 ASN C 309 HIS D 63 ASN D 309 HIS E 63 ASN E 155 ASN E 263 ASN E 309 HIS F 63 ASN F 78 ASN F 309 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.096427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.085478 restraints weight = 21345.217| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.08 r_work: 0.2842 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16422 Z= 0.132 Angle : 0.492 5.967 22326 Z= 0.255 Chirality : 0.043 0.132 2520 Planarity : 0.003 0.032 2952 Dihedral : 5.709 74.022 2281 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.01 % Allowed : 13.89 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.16), residues: 2076 helix: -2.25 (0.43), residues: 126 sheet: -1.24 (0.15), residues: 888 loop : -1.42 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 234 TYR 0.011 0.001 TYR E 281 PHE 0.010 0.002 PHE E 7 TRP 0.003 0.001 TRP F 173 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00303 (16422) covalent geometry : angle 0.49169 (22326) hydrogen bonds : bond 0.03764 ( 120) hydrogen bonds : angle 4.12119 ( 324) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.565 Fit side-chains REVERT: B 288 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8653 (ttpp) REVERT: C 288 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8534 (ttpp) REVERT: D 48 ARG cc_start: 0.8390 (mtm180) cc_final: 0.7428 (ppt170) REVERT: D 67 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: D 98 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7264 (t70) REVERT: D 243 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7952 (mm-30) REVERT: E 48 ARG cc_start: 0.8326 (mtm180) cc_final: 0.7302 (ppt170) REVERT: F 48 ARG cc_start: 0.8287 (mtm180) cc_final: 0.7291 (ppt170) REVERT: F 67 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7187 (mt-10) outliers start: 51 outliers final: 14 residues processed: 187 average time/residue: 0.6625 time to fit residues: 134.8856 Evaluate side-chains 144 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 4 optimal weight: 0.0980 chunk 127 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN D 78 ASN E 46 GLN E 78 ASN E 155 ASN F 221 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.084233 restraints weight = 21603.899| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.08 r_work: 0.2819 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16422 Z= 0.180 Angle : 0.515 5.872 22326 Z= 0.265 Chirality : 0.043 0.135 2520 Planarity : 0.004 0.038 2952 Dihedral : 5.727 82.566 2277 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.90 % Allowed : 15.90 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.17), residues: 2076 helix: -1.85 (0.45), residues: 126 sheet: -0.81 (0.16), residues: 900 loop : -1.21 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 314 TYR 0.012 0.001 TYR B 130 PHE 0.025 0.002 PHE F 214 TRP 0.002 0.001 TRP E 173 HIS 0.002 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00424 (16422) covalent geometry : angle 0.51457 (22326) hydrogen bonds : bond 0.03859 ( 120) hydrogen bonds : angle 4.10584 ( 324) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.639 Fit side-chains REVERT: B 288 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8685 (ttpp) REVERT: D 46 GLN cc_start: 0.8289 (tp40) cc_final: 0.7875 (tp40) REVERT: D 48 ARG cc_start: 0.8431 (mtm180) cc_final: 0.7337 (ppt170) REVERT: D 67 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6908 (mt-10) REVERT: D 73 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: D 98 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7245 (t70) REVERT: D 243 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7895 (mm-30) REVERT: E 43 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: E 48 ARG cc_start: 0.8368 (mtm180) cc_final: 0.7295 (ppt170) REVERT: E 73 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: F 48 ARG cc_start: 0.8348 (mtm180) cc_final: 0.7311 (ppt170) REVERT: F 67 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7087 (mt-10) outliers start: 49 outliers final: 16 residues processed: 172 average time/residue: 0.6439 time to fit residues: 120.4804 Evaluate side-chains 151 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 3 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.3980 chunk 172 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN D 78 ASN E 46 GLN E 78 ASN E 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.094761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.083816 restraints weight = 21629.824| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.07 r_work: 0.2817 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16422 Z= 0.183 Angle : 0.513 5.759 22326 Z= 0.264 Chirality : 0.043 0.134 2520 Planarity : 0.004 0.040 2952 Dihedral : 5.464 87.897 2274 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.49 % Allowed : 15.19 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.39 (0.17), residues: 2076 helix: -1.61 (0.45), residues: 126 sheet: -0.59 (0.16), residues: 900 loop : -1.04 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 314 TYR 0.012 0.001 TYR B 130 PHE 0.013 0.002 PHE B 248 TRP 0.003 0.001 TRP A 173 HIS 0.002 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00431 (16422) covalent geometry : angle 0.51321 (22326) hydrogen bonds : bond 0.03773 ( 120) hydrogen bonds : angle 4.12303 ( 324) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 0.510 Fit side-chains REVERT: B 73 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: B 151 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8867 (mtt) REVERT: B 208 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: B 276 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7934 (mm-30) REVERT: B 288 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8683 (ttpp) REVERT: C 73 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: C 206 LEU cc_start: 0.9230 (mt) cc_final: 0.9014 (mt) REVERT: D 46 GLN cc_start: 0.8273 (tp40) cc_final: 0.7856 (tp40) REVERT: D 48 ARG cc_start: 0.8444 (mtm180) cc_final: 0.7361 (ppt170) REVERT: D 67 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: D 73 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: D 98 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7267 (t70) REVERT: D 243 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7883 (mm-30) REVERT: E 36 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: E 43 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: E 48 ARG cc_start: 0.8348 (mtm180) cc_final: 0.7281 (ppt170) REVERT: E 73 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: F 48 ARG cc_start: 0.8309 (mtm180) cc_final: 0.7290 (ppt170) REVERT: F 67 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: F 73 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: F 239 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8290 (pm20) outliers start: 59 outliers final: 22 residues processed: 183 average time/residue: 0.6639 time to fit residues: 131.8905 Evaluate side-chains 167 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.4980 chunk 194 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 49 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 175 ASN D 13 GLN D 78 ASN E 13 GLN E 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.086202 restraints weight = 21586.716| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.07 r_work: 0.2854 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 16422 Z= 0.110 Angle : 0.461 5.419 22326 Z= 0.236 Chirality : 0.042 0.128 2520 Planarity : 0.003 0.036 2952 Dihedral : 5.163 89.597 2274 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.90 % Allowed : 16.08 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.17), residues: 2076 helix: -1.26 (0.47), residues: 126 sheet: -0.58 (0.16), residues: 924 loop : -0.91 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.009 0.001 TYR B 130 PHE 0.030 0.002 PHE F 214 TRP 0.003 0.001 TRP B 173 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00255 (16422) covalent geometry : angle 0.46110 (22326) hydrogen bonds : bond 0.02962 ( 120) hydrogen bonds : angle 3.94436 ( 324) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.481 Fit side-chains REVERT: B 203 MET cc_start: 0.9315 (mtp) cc_final: 0.9074 (mtp) REVERT: B 276 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: B 288 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8675 (ttpp) REVERT: C 206 LEU cc_start: 0.9206 (mt) cc_final: 0.8983 (mt) REVERT: C 276 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: D 46 GLN cc_start: 0.8179 (tp40) cc_final: 0.7768 (tp40) REVERT: D 48 ARG cc_start: 0.8469 (mtm180) cc_final: 0.7357 (ppt170) REVERT: D 67 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: D 73 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: D 98 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7311 (t70) REVERT: D 243 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7924 (mm-30) REVERT: E 48 ARG cc_start: 0.8295 (mtm180) cc_final: 0.7227 (ppt170) REVERT: F 48 ARG cc_start: 0.8281 (mtm180) cc_final: 0.7278 (ppt170) REVERT: F 239 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8210 (pm20) outliers start: 49 outliers final: 19 residues processed: 188 average time/residue: 0.6736 time to fit residues: 137.6571 Evaluate side-chains 160 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 130 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 GLN E 155 ASN E 221 ASN F 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.094906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.084078 restraints weight = 21516.608| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.09 r_work: 0.2820 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16422 Z= 0.202 Angle : 0.523 5.577 22326 Z= 0.269 Chirality : 0.044 0.137 2520 Planarity : 0.004 0.039 2952 Dihedral : 5.465 87.187 2274 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.43 % Allowed : 15.37 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.17), residues: 2076 helix: -1.31 (0.46), residues: 126 sheet: -0.38 (0.16), residues: 900 loop : -0.85 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.012 0.002 TYR F 130 PHE 0.026 0.002 PHE B 214 TRP 0.002 0.001 TRP A 173 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00477 (16422) covalent geometry : angle 0.52341 (22326) hydrogen bonds : bond 0.03723 ( 120) hydrogen bonds : angle 4.14977 ( 324) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 0.430 Fit side-chains REVERT: A 36 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6661 (tm-30) REVERT: A 208 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: B 73 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: B 151 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8856 (mtt) REVERT: B 208 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: B 276 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: B 288 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8699 (ttpp) REVERT: C 73 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: C 206 LEU cc_start: 0.9237 (mt) cc_final: 0.9012 (mt) REVERT: D 36 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: D 46 GLN cc_start: 0.8254 (tp40) cc_final: 0.7827 (tp40) REVERT: D 48 ARG cc_start: 0.8462 (mtm180) cc_final: 0.7386 (ppt170) REVERT: D 67 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: D 73 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: D 98 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7335 (t70) REVERT: D 208 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: D 243 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7913 (mm-30) REVERT: E 36 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: E 48 ARG cc_start: 0.8353 (mtm180) cc_final: 0.7318 (ppt170) REVERT: E 208 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8431 (tm-30) REVERT: E 239 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: F 48 ARG cc_start: 0.8366 (mtm180) cc_final: 0.7304 (ppt170) REVERT: F 67 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: F 73 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: F 239 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8230 (pm20) outliers start: 58 outliers final: 21 residues processed: 183 average time/residue: 0.6913 time to fit residues: 137.1500 Evaluate side-chains 167 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 195 optimal weight: 0.0570 chunk 159 optimal weight: 5.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 ASN D 78 ASN E 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.096499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.085764 restraints weight = 21305.674| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.08 r_work: 0.2846 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16422 Z= 0.131 Angle : 0.473 5.320 22326 Z= 0.242 Chirality : 0.042 0.129 2520 Planarity : 0.004 0.037 2952 Dihedral : 5.236 89.590 2274 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.13 % Allowed : 15.90 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.17), residues: 2076 helix: -1.14 (0.47), residues: 126 sheet: -0.44 (0.16), residues: 924 loop : -0.76 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.010 0.001 TYR B 130 PHE 0.031 0.002 PHE F 214 TRP 0.003 0.001 TRP D 173 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00305 (16422) covalent geometry : angle 0.47290 (22326) hydrogen bonds : bond 0.03104 ( 120) hydrogen bonds : angle 4.03154 ( 324) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 0.502 Fit side-chains REVERT: A 36 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: B 73 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: B 151 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8869 (mtt) REVERT: B 276 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: B 288 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8679 (ttpp) REVERT: C 73 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: C 206 LEU cc_start: 0.9201 (mt) cc_final: 0.8990 (mt) REVERT: D 46 GLN cc_start: 0.8161 (tp40) cc_final: 0.7738 (tp40) REVERT: D 48 ARG cc_start: 0.8460 (mtm180) cc_final: 0.7392 (ppt170) REVERT: D 67 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: D 73 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: D 98 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7281 (t70) REVERT: D 243 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7901 (mm-30) REVERT: E 48 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7288 (ppt170) REVERT: E 73 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: E 239 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: F 48 ARG cc_start: 0.8346 (mtm180) cc_final: 0.7124 (ppt170) REVERT: F 67 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: F 239 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8219 (pm20) outliers start: 53 outliers final: 21 residues processed: 181 average time/residue: 0.6663 time to fit residues: 130.9579 Evaluate side-chains 165 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 203 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.084764 restraints weight = 21436.964| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.08 r_work: 0.2833 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16422 Z= 0.171 Angle : 0.505 5.381 22326 Z= 0.260 Chirality : 0.043 0.189 2520 Planarity : 0.004 0.038 2952 Dihedral : 4.921 84.321 2271 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.01 % Allowed : 15.84 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.17), residues: 2076 helix: -1.17 (0.46), residues: 126 sheet: -0.29 (0.16), residues: 900 loop : -0.73 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.011 0.001 TYR D 130 PHE 0.028 0.002 PHE B 214 TRP 0.002 0.001 TRP C 173 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00401 (16422) covalent geometry : angle 0.50463 (22326) hydrogen bonds : bond 0.03405 ( 120) hydrogen bonds : angle 4.13060 ( 324) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.649 Fit side-chains REVERT: A 36 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: A 208 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: B 73 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: B 151 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8868 (mtt) REVERT: B 208 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: B 276 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7897 (mm-30) REVERT: B 288 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8698 (ttpp) REVERT: C 73 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: C 206 LEU cc_start: 0.9217 (mt) cc_final: 0.8994 (mt) REVERT: D 36 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6611 (tm-30) REVERT: D 46 GLN cc_start: 0.8187 (tp40) cc_final: 0.7746 (tp40) REVERT: D 48 ARG cc_start: 0.8484 (mtm180) cc_final: 0.7401 (ppt170) REVERT: D 67 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6896 (mt-10) REVERT: D 73 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: D 98 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7270 (t70) REVERT: D 243 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7916 (mm-30) REVERT: E 36 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6534 (tm-30) REVERT: E 48 ARG cc_start: 0.8385 (mtm180) cc_final: 0.7304 (ppt170) REVERT: E 73 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: E 208 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8444 (tm-30) REVERT: E 239 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: F 48 ARG cc_start: 0.8354 (mtm180) cc_final: 0.7135 (ppt170) REVERT: F 67 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6882 (mt-10) REVERT: F 239 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8213 (pm20) outliers start: 51 outliers final: 21 residues processed: 178 average time/residue: 0.7223 time to fit residues: 139.1079 Evaluate side-chains 166 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 200 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 65 optimal weight: 0.4980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN B 13 GLN E 155 ASN F 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.086762 restraints weight = 21422.350| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.07 r_work: 0.2864 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16422 Z= 0.107 Angle : 0.458 5.753 22326 Z= 0.235 Chirality : 0.042 0.174 2520 Planarity : 0.003 0.035 2952 Dihedral : 4.601 83.828 2271 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.30 % Allowed : 16.55 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.17), residues: 2076 helix: -0.99 (0.47), residues: 126 sheet: -0.35 (0.16), residues: 924 loop : -0.67 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.009 0.001 TYR B 130 PHE 0.032 0.002 PHE E 214 TRP 0.003 0.001 TRP A 173 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00247 (16422) covalent geometry : angle 0.45769 (22326) hydrogen bonds : bond 0.02691 ( 120) hydrogen bonds : angle 3.97725 ( 324) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.591 Fit side-chains REVERT: A 36 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: B 151 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8856 (mtt) REVERT: B 276 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7831 (mm-30) REVERT: B 288 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8694 (ttpp) REVERT: C 206 LEU cc_start: 0.9174 (mt) cc_final: 0.8963 (mt) REVERT: C 208 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: D 46 GLN cc_start: 0.8136 (tp40) cc_final: 0.7701 (tp40) REVERT: D 48 ARG cc_start: 0.8473 (mtm180) cc_final: 0.7365 (ppt170) REVERT: D 67 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6853 (mt-10) REVERT: D 73 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: D 98 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7272 (t70) REVERT: D 243 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7950 (mm-30) REVERT: E 48 ARG cc_start: 0.8358 (mtm180) cc_final: 0.7287 (ppt170) REVERT: F 48 ARG cc_start: 0.8321 (mtm180) cc_final: 0.7094 (ppt170) REVERT: F 67 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: F 239 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8199 (pm20) outliers start: 39 outliers final: 22 residues processed: 168 average time/residue: 0.7209 time to fit residues: 131.4131 Evaluate side-chains 158 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 91 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 168 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 ASN E 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.087241 restraints weight = 21202.777| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.07 r_work: 0.2870 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16422 Z= 0.108 Angle : 0.460 6.330 22326 Z= 0.237 Chirality : 0.042 0.166 2520 Planarity : 0.003 0.035 2952 Dihedral : 4.540 83.803 2271 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.25 % Allowed : 16.78 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2076 helix: -0.90 (0.48), residues: 126 sheet: -0.30 (0.16), residues: 924 loop : -0.63 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 41 TYR 0.009 0.001 TYR F 130 PHE 0.031 0.001 PHE B 214 TRP 0.004 0.001 TRP A 173 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00250 (16422) covalent geometry : angle 0.46036 (22326) hydrogen bonds : bond 0.02638 ( 120) hydrogen bonds : angle 3.97821 ( 324) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.849 Fit side-chains REVERT: A 36 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: B 73 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: B 151 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8833 (mtt) REVERT: B 203 MET cc_start: 0.9279 (mtp) cc_final: 0.8968 (mtp) REVERT: B 208 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: B 276 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7830 (mm-30) REVERT: B 288 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8708 (ttpp) REVERT: C 206 LEU cc_start: 0.9186 (mt) cc_final: 0.8983 (mt) REVERT: C 208 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: D 46 GLN cc_start: 0.8148 (tp40) cc_final: 0.7723 (tp40) REVERT: D 48 ARG cc_start: 0.8467 (mtm180) cc_final: 0.7370 (ppt170) REVERT: D 67 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6849 (mt-10) REVERT: D 73 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: D 98 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7199 (t70) REVERT: D 243 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7980 (mm-30) REVERT: E 48 ARG cc_start: 0.8342 (mtm180) cc_final: 0.7290 (ppt170) REVERT: F 48 ARG cc_start: 0.8312 (mtm180) cc_final: 0.7101 (ppt170) REVERT: F 67 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6873 (mt-10) REVERT: F 239 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8185 (pm20) outliers start: 38 outliers final: 20 residues processed: 162 average time/residue: 0.6909 time to fit residues: 121.7275 Evaluate side-chains 161 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 93 optimal weight: 0.0170 chunk 133 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.096880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.086048 restraints weight = 21267.233| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.06 r_work: 0.2852 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16422 Z= 0.128 Angle : 0.471 6.044 22326 Z= 0.242 Chirality : 0.042 0.161 2520 Planarity : 0.004 0.037 2952 Dihedral : 4.179 17.376 2268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.36 % Allowed : 16.61 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.17), residues: 2076 helix: -0.89 (0.47), residues: 126 sheet: -0.26 (0.16), residues: 924 loop : -0.62 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 41 TYR 0.010 0.001 TYR F 130 PHE 0.033 0.002 PHE E 214 TRP 0.003 0.001 TRP B 173 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00299 (16422) covalent geometry : angle 0.47116 (22326) hydrogen bonds : bond 0.02767 ( 120) hydrogen bonds : angle 3.98806 ( 324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3890.41 seconds wall clock time: 67 minutes 20.30 seconds (4040.30 seconds total)