Starting phenix.real_space_refine on Sat Jun 14 06:37:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8edx_28042/06_2025/8edx_28042.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edx_28042/06_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_28042/06_2025/8edx_28042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edx_28042/06_2025/8edx_28042.map" model { file = "/net/cci-nas-00/data/ceres_data/8edx_28042/06_2025/8edx_28042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edx_28042/06_2025/8edx_28042.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.46, per 1000 atoms: 0.59 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: 3.68 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.60 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: 3.86 Time building geometry restraints manager: 4.41 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.840 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (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 TRP 0.002 0.001 TRP B 173 HIS 0.003 0.001 HIS F 220 PHE 0.014 0.002 PHE F 214 TYR 0.014 0.002 TYR E 337 ARG 0.004 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.19009 ( 120) hydrogen bonds : angle 6.51844 ( 324) covalent geometry : bond 0.00589 (16422) covalent geometry : angle 0.59773 (22326) *********************** 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 : 1.986 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: 1.8472 time to fit residues: 333.8305 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 : 1.899 ------------------------------------------------------------------------------- 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 172 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 0.0570 chunk 185 optimal weight: 6.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- 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 13 GLN E 63 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 = 0.3080 r_free = 0.3080 target = 0.097026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.085987 restraints weight = 21250.332| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.07 r_work: 0.2849 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16422 Z= 0.121 Angle : 0.486 5.879 22326 Z= 0.252 Chirality : 0.043 0.132 2520 Planarity : 0.003 0.031 2952 Dihedral : 5.670 73.045 2281 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.96 % Allowed : 13.71 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.16), residues: 2076 helix: -2.25 (0.44), residues: 126 sheet: -1.26 (0.15), residues: 888 loop : -1.41 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 173 HIS 0.003 0.001 HIS A 309 PHE 0.010 0.001 PHE B 89 TYR 0.011 0.001 TYR F 60 ARG 0.002 0.000 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 120) hydrogen bonds : angle 4.15757 ( 324) covalent geometry : bond 0.00275 (16422) covalent geometry : angle 0.48603 (22326) *********************** 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 201 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 1.762 Fit side-chains REVERT: B 288 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8654 (ttpp) REVERT: C 288 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8546 (ttpp) REVERT: D 48 ARG cc_start: 0.8409 (mtm180) cc_final: 0.7394 (ppt170) REVERT: D 67 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: D 98 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7251 (t70) REVERT: D 243 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7907 (mm-30) REVERT: E 48 ARG cc_start: 0.8325 (mtm180) cc_final: 0.7381 (ppt170) REVERT: F 48 ARG cc_start: 0.8297 (mtm180) cc_final: 0.7264 (ppt170) REVERT: F 67 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7152 (mt-10) outliers start: 50 outliers final: 14 residues processed: 190 average time/residue: 1.5785 time to fit residues: 327.2236 Evaluate side-chains 143 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 44 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 79 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 13 GLN D 78 ASN E 46 GLN E 78 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 = 0.3085 r_free = 0.3085 target = 0.097294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.086448 restraints weight = 21395.451| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.06 r_work: 0.2859 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16422 Z= 0.112 Angle : 0.466 5.548 22326 Z= 0.239 Chirality : 0.042 0.130 2520 Planarity : 0.003 0.033 2952 Dihedral : 5.337 77.445 2277 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.13 % Allowed : 16.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 2076 helix: -1.75 (0.46), residues: 126 sheet: -0.90 (0.16), residues: 888 loop : -1.12 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 173 HIS 0.003 0.000 HIS B 309 PHE 0.026 0.002 PHE E 214 TYR 0.010 0.001 TYR D 60 ARG 0.003 0.000 ARG B 305 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 120) hydrogen bonds : angle 3.92968 ( 324) covalent geometry : bond 0.00261 (16422) covalent geometry : angle 0.46585 (22326) *********************** 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 179 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.847 Fit side-chains REVERT: B 203 MET cc_start: 0.9342 (mtp) cc_final: 0.8982 (mtp) REVERT: B 288 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8673 (ttpp) REVERT: D 46 GLN cc_start: 0.8272 (tp40) cc_final: 0.7869 (tp40) REVERT: D 48 ARG cc_start: 0.8379 (mtm180) cc_final: 0.7277 (ppt170) REVERT: D 67 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: D 98 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7260 (t70) REVERT: D 243 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7958 (mm-30) REVERT: E 48 ARG cc_start: 0.8358 (mtm180) cc_final: 0.7297 (ppt170) REVERT: F 48 ARG cc_start: 0.8251 (mtm180) cc_final: 0.7278 (ppt170) outliers start: 36 outliers final: 15 residues processed: 170 average time/residue: 1.5130 time to fit residues: 281.3047 Evaluate side-chains 152 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 67 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 190 VAL Chi-restraints excluded: chain E residue 254 VAL 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 1 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 199 optimal weight: 0.0050 overall best weight: 2.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 ASN E 46 GLN E 221 ASN E 263 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 = 0.094888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.084017 restraints weight = 21465.555| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.09 r_work: 0.2819 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16422 Z= 0.196 Angle : 0.524 5.707 22326 Z= 0.270 Chirality : 0.044 0.138 2520 Planarity : 0.004 0.038 2952 Dihedral : 4.602 17.980 2268 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.43 % Allowed : 15.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2076 helix: -1.67 (0.45), residues: 126 sheet: -0.19 (0.17), residues: 786 loop : -1.22 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 173 HIS 0.002 0.001 HIS A 309 PHE 0.022 0.002 PHE B 214 TYR 0.012 0.002 TYR B 130 ARG 0.003 0.000 ARG D 234 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 120) hydrogen bonds : angle 4.14419 ( 324) covalent geometry : bond 0.00464 (16422) covalent geometry : angle 0.52433 (22326) *********************** 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 197 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 1.991 Fit side-chains REVERT: B 73 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: B 151 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8866 (mtt) REVERT: B 288 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8689 (ttpp) REVERT: C 73 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: C 206 LEU cc_start: 0.9241 (mt) cc_final: 0.9018 (mt) REVERT: D 36 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6545 (tm-30) REVERT: D 46 GLN cc_start: 0.8305 (tp40) cc_final: 0.7895 (tp40) REVERT: D 48 ARG cc_start: 0.8444 (mtm180) cc_final: 0.7377 (ppt170) REVERT: D 67 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: D 98 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7302 (t70) REVERT: D 239 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: D 243 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7890 (mm-30) REVERT: E 36 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: E 48 ARG cc_start: 0.8345 (mtm180) cc_final: 0.7349 (ppt170) REVERT: E 73 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: F 48 ARG cc_start: 0.8310 (mtm180) cc_final: 0.7305 (ppt170) REVERT: F 67 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: F 239 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8222 (pm20) outliers start: 58 outliers final: 22 residues processed: 186 average time/residue: 1.6216 time to fit residues: 328.1375 Evaluate side-chains 162 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 254 VAL 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 36 GLU 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 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 239 GLU 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 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 163 optimal weight: 8.9990 chunk 152 optimal weight: 0.0870 chunk 138 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 overall best weight: 4.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.096864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.085230 restraints weight = 20192.613| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.15 r_work: 0.2807 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 16422 Z= 0.307 Angle : 0.603 6.019 22326 Z= 0.311 Chirality : 0.047 0.157 2520 Planarity : 0.005 0.058 2952 Dihedral : 5.062 18.834 2268 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.61 % Allowed : 15.01 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2076 helix: -1.60 (0.46), residues: 120 sheet: -0.41 (0.16), residues: 906 loop : -0.96 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP A 173 HIS 0.003 0.001 HIS A 309 PHE 0.027 0.003 PHE E 214 TYR 0.014 0.002 TYR B 130 ARG 0.005 0.001 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 120) hydrogen bonds : angle 4.44677 ( 324) covalent geometry : bond 0.00730 (16422) covalent geometry : angle 0.60309 (22326) *********************** 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 188 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 127 time to evaluate : 1.958 Fit side-chains REVERT: B 73 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: B 151 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8784 (mtt) REVERT: B 208 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8339 (tm-30) REVERT: B 288 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8776 (ttpp) REVERT: C 73 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8056 (tm-30) REVERT: D 36 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: D 46 GLN cc_start: 0.8285 (tp40) cc_final: 0.7815 (tp40) REVERT: D 48 ARG cc_start: 0.8597 (mtm180) cc_final: 0.7356 (ppt170) REVERT: D 67 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: D 73 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: D 98 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7503 (t70) REVERT: D 243 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7924 (mm-30) REVERT: E 36 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: E 48 ARG cc_start: 0.8494 (mtm180) cc_final: 0.7272 (ppt170) REVERT: E 73 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: E 239 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: F 48 ARG cc_start: 0.8517 (mtm180) cc_final: 0.7309 (ppt170) REVERT: F 67 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: F 73 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: F 239 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8292 (pm20) outliers start: 61 outliers final: 23 residues processed: 180 average time/residue: 1.6228 time to fit residues: 318.4253 Evaluate side-chains 156 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 238 ASP Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 VAL 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 190 VAL Chi-restraints excluded: chain D residue 247 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 7 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 188 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN C 175 ASN D 78 ASN E 46 GLN E 78 ASN E 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.096093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.085382 restraints weight = 21355.003| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.06 r_work: 0.2842 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16422 Z= 0.127 Angle : 0.479 5.507 22326 Z= 0.247 Chirality : 0.042 0.127 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.452 18.377 2268 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.60 % Allowed : 15.96 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2076 helix: -1.32 (0.46), residues: 126 sheet: 0.01 (0.17), residues: 786 loop : -1.07 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 173 HIS 0.002 0.000 HIS A 309 PHE 0.027 0.001 PHE B 214 TYR 0.010 0.001 TYR B 130 ARG 0.001 0.000 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 120) hydrogen bonds : angle 4.04698 ( 324) covalent geometry : bond 0.00288 (16422) covalent geometry : angle 0.47857 (22326) *********************** 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 179 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.900 Fit side-chains REVERT: A 36 GLU cc_start: 0.7876 (pp20) cc_final: 0.7661 (tm-30) REVERT: A 208 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: B 288 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8658 (ttpp) REVERT: C 206 LEU cc_start: 0.9228 (mt) cc_final: 0.9004 (mt) REVERT: D 46 GLN cc_start: 0.8183 (tp40) cc_final: 0.7774 (tp40) REVERT: D 48 ARG cc_start: 0.8456 (mtm180) cc_final: 0.7369 (ppt170) REVERT: D 67 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: D 73 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: D 98 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7326 (t70) REVERT: D 243 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7955 (mm-30) REVERT: E 43 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: E 48 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7275 (ppt170) REVERT: F 48 ARG cc_start: 0.8322 (mtm180) cc_final: 0.7281 (ppt170) REVERT: F 67 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: F 239 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8214 (pm20) outliers start: 44 outliers final: 19 residues processed: 171 average time/residue: 1.5263 time to fit residues: 285.3034 Evaluate side-chains 154 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 247 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 43 GLN 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 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 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 43 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 41 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 93 optimal weight: 0.0670 chunk 108 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 162 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 171 optimal weight: 0.8980 overall best weight: 0.6110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 175 ASN D 13 GLN F 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.098976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.088325 restraints weight = 21370.370| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.07 r_work: 0.2892 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16422 Z= 0.085 Angle : 0.440 5.172 22326 Z= 0.226 Chirality : 0.041 0.126 2520 Planarity : 0.003 0.034 2952 Dihedral : 4.001 18.065 2268 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.42 % Allowed : 16.67 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2076 helix: -0.98 (0.48), residues: 126 sheet: -0.47 (0.16), residues: 912 loop : -0.68 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 173 HIS 0.001 0.000 HIS A 309 PHE 0.032 0.001 PHE E 214 TYR 0.008 0.001 TYR D 130 ARG 0.004 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.02379 ( 120) hydrogen bonds : angle 3.88052 ( 324) covalent geometry : bond 0.00194 (16422) covalent geometry : angle 0.44032 (22326) *********************** 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 190 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.817 Fit side-chains REVERT: B 203 MET cc_start: 0.9303 (mtp) cc_final: 0.9002 (mtp) REVERT: C 206 LEU cc_start: 0.9174 (mt) cc_final: 0.8951 (mt) REVERT: D 46 GLN cc_start: 0.8137 (tp40) cc_final: 0.7737 (tp40) REVERT: D 67 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6860 (mt-10) REVERT: D 73 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: D 98 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7317 (t70) REVERT: D 243 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7988 (mm-30) REVERT: E 48 ARG cc_start: 0.8306 (mtm180) cc_final: 0.7222 (ppt170) REVERT: F 48 ARG cc_start: 0.8255 (mtm180) cc_final: 0.7131 (ppt170) REVERT: F 239 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8212 (pm20) outliers start: 41 outliers final: 15 residues processed: 182 average time/residue: 1.4493 time to fit residues: 289.5470 Evaluate side-chains 155 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL 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 313 VAL Chi-restraints excluded: chain C residue 190 VAL 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 E residue 190 VAL Chi-restraints excluded: chain E residue 254 VAL 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 177 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 64 optimal weight: 0.0370 chunk 120 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 178 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.096327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.085435 restraints weight = 21480.356| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.10 r_work: 0.2842 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1848 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= 0.154 Angle : 0.497 5.436 22326 Z= 0.256 Chirality : 0.043 0.181 2520 Planarity : 0.004 0.037 2952 Dihedral : 4.338 18.570 2268 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.25 % Allowed : 17.14 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2076 helix: -1.01 (0.47), residues: 126 sheet: -0.26 (0.16), residues: 900 loop : -0.66 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 173 HIS 0.002 0.001 HIS A 309 PHE 0.028 0.002 PHE B 214 TYR 0.012 0.001 TYR F 130 ARG 0.003 0.000 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 120) hydrogen bonds : angle 4.04077 ( 324) covalent geometry : bond 0.00361 (16422) covalent geometry : angle 0.49701 (22326) *********************** 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 174 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.779 Fit side-chains REVERT: A 36 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: A 208 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: B 208 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: C 206 LEU cc_start: 0.9231 (mt) cc_final: 0.9007 (mt) REVERT: D 46 GLN cc_start: 0.8203 (tp40) cc_final: 0.7769 (tp40) REVERT: D 48 ARG cc_start: 0.8457 (mtm180) cc_final: 0.7376 (ppt170) REVERT: D 67 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: D 73 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: D 98 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7266 (t70) REVERT: D 243 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7950 (mm-30) REVERT: E 48 ARG cc_start: 0.8395 (mtm180) cc_final: 0.7269 (ppt170) REVERT: E 208 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: F 48 ARG cc_start: 0.8350 (mtm180) cc_final: 0.7140 (ppt170) REVERT: F 239 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8216 (pm20) outliers start: 38 outliers final: 19 residues processed: 170 average time/residue: 1.5878 time to fit residues: 296.0011 Evaluate side-chains 156 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 98 ASP 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 313 VAL Chi-restraints excluded: chain C residue 190 VAL 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 313 VAL 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 254 VAL 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 88 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 133 optimal weight: 0.2980 chunk 181 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN D 78 ASN E 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.095175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.084352 restraints weight = 21363.447| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.08 r_work: 0.2826 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1807 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= 0.189 Angle : 0.527 5.495 22326 Z= 0.271 Chirality : 0.044 0.180 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.578 18.983 2268 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.54 % Allowed : 16.84 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2076 helix: -1.16 (0.46), residues: 126 sheet: -0.22 (0.16), residues: 900 loop : -0.68 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 173 HIS 0.002 0.001 HIS A 309 PHE 0.031 0.002 PHE F 214 TYR 0.012 0.002 TYR F 130 ARG 0.003 0.000 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 120) hydrogen bonds : angle 4.16492 ( 324) covalent geometry : bond 0.00445 (16422) covalent geometry : angle 0.52712 (22326) *********************** 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 172 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.757 Fit side-chains REVERT: A 36 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: A 208 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: B 208 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: C 206 LEU cc_start: 0.9242 (mt) cc_final: 0.9021 (mt) REVERT: D 46 GLN cc_start: 0.8184 (tp40) cc_final: 0.7742 (tp40) REVERT: D 48 ARG cc_start: 0.8489 (mtm180) cc_final: 0.7370 (ppt170) REVERT: D 67 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6894 (mt-10) REVERT: D 73 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: D 98 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7355 (t70) REVERT: D 243 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7922 (mm-30) REVERT: E 36 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: E 48 ARG cc_start: 0.8419 (mtm180) cc_final: 0.7283 (ppt170) REVERT: E 208 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: F 48 ARG cc_start: 0.8358 (mtm180) cc_final: 0.7287 (ppt170) REVERT: F 239 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8262 (pm20) outliers start: 43 outliers final: 20 residues processed: 166 average time/residue: 1.6095 time to fit residues: 290.7328 Evaluate side-chains 155 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 247 THR 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 208 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 190 VAL 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 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 254 VAL 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 26 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.096232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.085353 restraints weight = 21565.365| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.10 r_work: 0.2841 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16422 Z= 0.142 Angle : 0.492 5.365 22326 Z= 0.254 Chirality : 0.043 0.172 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.388 18.563 2268 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.83 % Allowed : 17.43 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2076 helix: -1.05 (0.47), residues: 126 sheet: -0.21 (0.17), residues: 900 loop : -0.66 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 173 HIS 0.002 0.001 HIS A 309 PHE 0.031 0.001 PHE B 214 TYR 0.011 0.001 TYR F 130 ARG 0.003 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 120) hydrogen bonds : angle 4.08786 ( 324) covalent geometry : bond 0.00332 (16422) covalent geometry : angle 0.49169 (22326) ********************** 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 158 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 2.021 Fit side-chains REVERT: A 36 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: A 208 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8291 (tm-30) REVERT: B 208 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: C 206 LEU cc_start: 0.9232 (mt) cc_final: 0.9006 (mt) REVERT: D 46 GLN cc_start: 0.8173 (tp40) cc_final: 0.7751 (tp40) REVERT: D 48 ARG cc_start: 0.8468 (mtm180) cc_final: 0.7398 (ppt170) REVERT: D 67 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6885 (mt-10) REVERT: D 73 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: D 98 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7339 (t70) REVERT: D 243 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7960 (mm-30) REVERT: E 48 ARG cc_start: 0.8390 (mtm180) cc_final: 0.7328 (ppt170) REVERT: E 208 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: F 48 ARG cc_start: 0.8339 (mtm180) cc_final: 0.7150 (ppt170) REVERT: F 239 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8263 (pm20) outliers start: 31 outliers final: 19 residues processed: 154 average time/residue: 1.6877 time to fit residues: 282.8999 Evaluate side-chains 151 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 247 THR 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 208 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 190 VAL 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 208 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 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 181 optimal weight: 7.9990 chunk 196 optimal weight: 0.0470 chunk 80 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.095392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.084537 restraints weight = 21460.624| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.09 r_work: 0.2827 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1839 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= 0.179 Angle : 0.516 5.486 22326 Z= 0.266 Chirality : 0.044 0.172 2520 Planarity : 0.004 0.041 2952 Dihedral : 4.539 18.918 2268 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.89 % Allowed : 17.26 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2076 helix: -1.14 (0.46), residues: 126 sheet: -0.18 (0.17), residues: 900 loop : -0.67 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 173 HIS 0.002 0.001 HIS A 309 PHE 0.032 0.002 PHE E 214 TYR 0.012 0.001 TYR D 130 ARG 0.003 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 120) hydrogen bonds : angle 4.17618 ( 324) covalent geometry : bond 0.00420 (16422) covalent geometry : angle 0.51633 (22326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9274.92 seconds wall clock time: 159 minutes 28.42 seconds (9568.42 seconds total)