Starting phenix.real_space_refine on Tue Dec 31 14:15:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8edx_28042/12_2024/8edx_28042.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edx_28042/12_2024/8edx_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_28042/12_2024/8edx_28042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edx_28042/12_2024/8edx_28042.map" model { file = "/net/cci-nas-00/data/ceres_data/8edx_28042/12_2024/8edx_28042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edx_28042/12_2024/8edx_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 11.57, per 1000 atoms: 0.72 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: 4.90 Conformation dependent library (CDL) restraints added in 3.2 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: 1.88 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: 4.94 Time building geometry restraints manager: 6.24 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.810 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.800 ------------------------------------------------------------------------------- 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= 0.393 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 *********************** 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 : 2.239 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: 1.8787 time to fit residues: 338.1903 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 : 2.004 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 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= 0.185 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 *********************** 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 : 2.033 Fit side-chains REVERT: B 288 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8641 (ttpp) REVERT: C 288 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8604 (ttpp) REVERT: D 48 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7567 (ppt170) REVERT: D 67 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: D 98 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7286 (t70) REVERT: D 243 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8097 (mm-30) REVERT: E 48 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7568 (ppt170) REVERT: E 164 ASP cc_start: 0.8301 (p0) cc_final: 0.8101 (p0) REVERT: F 48 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7428 (ppt170) REVERT: F 67 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7435 (mt-10) outliers start: 50 outliers final: 14 residues processed: 190 average time/residue: 1.6681 time to fit residues: 344.9113 Evaluate side-chains 144 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 102 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 200 optimal weight: 0.0770 chunk 165 optimal weight: 0.2980 chunk 184 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 overall best weight: 3.0744 ------------------------------------------------------------------------------- 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 78 ASN E 263 ASN F 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16422 Z= 0.351 Angle : 0.544 6.003 22326 Z= 0.280 Chirality : 0.044 0.144 2520 Planarity : 0.004 0.044 2952 Dihedral : 5.881 83.811 2277 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.96 % Allowed : 15.54 % Favored : 81.50 % 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: -1.64 (0.17), residues: 2076 helix: -1.90 (0.46), residues: 120 sheet: -0.74 (0.16), residues: 906 loop : -1.22 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 173 HIS 0.002 0.001 HIS B 309 PHE 0.025 0.002 PHE F 214 TYR 0.013 0.002 TYR B 130 ARG 0.003 0.000 ARG E 314 *********************** 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 185 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 1.947 Fit side-chains REVERT: B 288 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8700 (ttpp) REVERT: C 73 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: D 36 GLU cc_start: 0.7896 (pp20) cc_final: 0.7692 (pp20) REVERT: D 46 GLN cc_start: 0.8333 (tp40) cc_final: 0.7960 (tp40) REVERT: D 48 ARG cc_start: 0.8281 (mtm180) cc_final: 0.7493 (ppt170) REVERT: D 67 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: D 73 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: D 98 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7299 (t70) REVERT: D 243 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8011 (mm-30) REVERT: E 48 ARG cc_start: 0.8223 (mtm180) cc_final: 0.7464 (ppt170) REVERT: E 73 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: E 164 ASP cc_start: 0.8370 (p0) cc_final: 0.8169 (p0) REVERT: F 48 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7472 (ppt170) REVERT: F 67 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7379 (mt-10) outliers start: 50 outliers final: 17 residues processed: 175 average time/residue: 1.7671 time to fit residues: 336.7708 Evaluate side-chains 148 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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 73 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 0.0470 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- 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 78 ASN F 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1496 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= 0.228 Angle : 0.486 5.642 22326 Z= 0.250 Chirality : 0.042 0.131 2520 Planarity : 0.004 0.038 2952 Dihedral : 5.349 87.937 2274 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.01 % Allowed : 15.43 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2076 helix: -1.61 (0.45), residues: 126 sheet: -0.20 (0.17), residues: 786 loop : -1.24 (0.16), residues: 1164 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 0.011 0.002 PHE E 7 TYR 0.011 0.001 TYR B 130 ARG 0.002 0.000 ARG E 296 *********************** 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 186 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 2.078 Fit side-chains REVERT: B 73 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: B 151 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8881 (mtt) REVERT: B 288 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8677 (ttpp) REVERT: C 206 LEU cc_start: 0.9184 (mt) cc_final: 0.8972 (mt) REVERT: D 46 GLN cc_start: 0.8315 (tp40) cc_final: 0.7939 (tp40) REVERT: D 48 ARG cc_start: 0.8272 (mtm180) cc_final: 0.7491 (ppt170) REVERT: D 67 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: D 73 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: D 98 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7330 (t70) REVERT: E 48 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7472 (ppt170) REVERT: E 164 ASP cc_start: 0.8320 (p0) cc_final: 0.8113 (p0) REVERT: E 243 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8113 (mm-30) REVERT: F 48 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7420 (ppt170) REVERT: F 73 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: F 239 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8340 (pm20) outliers start: 51 outliers final: 17 residues processed: 177 average time/residue: 1.6638 time to fit residues: 320.8612 Evaluate side-chains 158 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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 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 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 239 GLU 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 164 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 ASN D 78 ASN D 221 ASN E 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 16422 Z= 0.394 Angle : 0.557 5.860 22326 Z= 0.287 Chirality : 0.045 0.147 2520 Planarity : 0.004 0.046 2952 Dihedral : 5.288 87.088 2271 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.43 % Allowed : 15.01 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2076 helix: -1.49 (0.47), residues: 120 sheet: -0.01 (0.17), residues: 774 loop : -1.21 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 173 HIS 0.002 0.001 HIS A 309 PHE 0.027 0.002 PHE E 214 TYR 0.014 0.002 TYR B 130 ARG 0.003 0.001 ARG D 314 *********************** 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 190 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 132 time to evaluate : 1.963 Fit side-chains REVERT: B 73 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: B 151 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8869 (mtt) REVERT: B 208 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8245 (tm-30) REVERT: B 288 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8714 (ttpp) REVERT: C 73 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: D 46 GLN cc_start: 0.8333 (tp40) cc_final: 0.7940 (tp40) REVERT: D 48 ARG cc_start: 0.8315 (mtm180) cc_final: 0.7514 (ppt170) REVERT: D 67 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: D 73 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: D 98 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7389 (t70) REVERT: E 36 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: E 48 ARG cc_start: 0.8255 (mtm180) cc_final: 0.7458 (ppt170) REVERT: E 73 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: E 164 ASP cc_start: 0.8409 (p0) cc_final: 0.8192 (p0) REVERT: E 208 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: E 239 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: F 48 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7472 (ppt170) REVERT: F 67 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: F 73 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: F 208 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8494 (tm-30) REVERT: F 239 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8382 (pm20) outliers start: 58 outliers final: 22 residues processed: 183 average time/residue: 1.6816 time to fit residues: 334.8860 Evaluate side-chains 160 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 2.021 ------------------------------------------------------------------------------- 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 110 ASN 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 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 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 D residue 288 LYS Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 38 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN C 13 GLN D 78 ASN E 155 ASN F 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 16422 Z= 0.234 Angle : 0.492 5.526 22326 Z= 0.253 Chirality : 0.042 0.131 2520 Planarity : 0.004 0.040 2952 Dihedral : 4.975 85.033 2271 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.90 % Allowed : 15.78 % 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: -1.01 (0.17), residues: 2076 helix: -1.30 (0.46), residues: 126 sheet: 0.02 (0.17), residues: 786 loop : -1.08 (0.16), residues: 1164 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 0.027 0.002 PHE B 214 TYR 0.011 0.001 TYR B 130 ARG 0.003 0.000 ARG A 41 *********************** 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 183 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 1.919 Fit side-chains REVERT: A 36 GLU cc_start: 0.8150 (pp20) cc_final: 0.7932 (tm-30) REVERT: B 73 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8348 (tm-30) REVERT: B 151 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8879 (mtt) REVERT: B 208 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: B 288 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8691 (ttpp) REVERT: D 46 GLN cc_start: 0.8274 (tp40) cc_final: 0.7894 (tp40) REVERT: D 48 ARG cc_start: 0.8290 (mtm180) cc_final: 0.7501 (ppt170) REVERT: D 67 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: D 73 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: D 98 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7359 (t70) REVERT: D 208 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: E 36 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: E 48 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7457 (ppt170) REVERT: E 164 ASP cc_start: 0.8319 (p0) cc_final: 0.8105 (p0) REVERT: E 239 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: E 243 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8099 (mm-30) REVERT: F 48 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7437 (ppt170) REVERT: F 67 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: F 73 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: F 239 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8333 (pm20) outliers start: 49 outliers final: 22 residues processed: 176 average time/residue: 1.7239 time to fit residues: 331.0894 Evaluate side-chains 162 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 151 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 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 208 GLU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.0170 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 175 ASN D 13 GLN D 78 ASN E 155 ASN F 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16422 Z= 0.151 Angle : 0.452 5.312 22326 Z= 0.231 Chirality : 0.041 0.128 2520 Planarity : 0.003 0.035 2952 Dihedral : 4.585 84.256 2271 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.13 % Allowed : 16.19 % Favored : 80.67 % 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: -0.86 (0.17), residues: 2076 helix: -1.03 (0.47), residues: 126 sheet: 0.08 (0.18), residues: 786 loop : -0.96 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.002 0.000 HIS A 309 PHE 0.032 0.001 PHE E 214 TYR 0.009 0.001 TYR D 130 ARG 0.002 0.000 ARG A 41 *********************** 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 198 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 1.868 Fit side-chains REVERT: B 203 MET cc_start: 0.9290 (mtp) cc_final: 0.9032 (mtp) REVERT: B 208 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8179 (tm-30) REVERT: D 46 GLN cc_start: 0.8217 (tp40) cc_final: 0.7833 (tp40) REVERT: D 48 ARG cc_start: 0.8250 (mtm180) cc_final: 0.7489 (ppt170) REVERT: D 67 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: D 98 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7326 (t70) REVERT: D 208 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: E 48 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7370 (ppt170) REVERT: E 164 ASP cc_start: 0.8249 (p0) cc_final: 0.8023 (p0) REVERT: F 48 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7248 (ppt170) REVERT: F 73 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8247 (tm-30) REVERT: F 239 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8304 (pm20) outliers start: 53 outliers final: 20 residues processed: 190 average time/residue: 1.5839 time to fit residues: 328.6066 Evaluate side-chains 160 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 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 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 208 GLU 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 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 0.0010 chunk 97 optimal weight: 0.0770 chunk 18 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 GLN E 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1929 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= 0.184 Angle : 0.467 5.166 22326 Z= 0.240 Chirality : 0.042 0.188 2520 Planarity : 0.003 0.034 2952 Dihedral : 4.615 83.753 2271 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.30 % Allowed : 16.96 % 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: -0.92 (0.17), residues: 2076 helix: -0.95 (0.47), residues: 126 sheet: -0.38 (0.16), residues: 924 loop : -0.67 (0.18), residues: 1026 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 0.029 0.001 PHE B 214 TYR 0.010 0.001 TYR F 130 ARG 0.002 0.000 ARG E 41 *********************** 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 176 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 2.141 Fit side-chains REVERT: A 36 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: B 203 MET cc_start: 0.9308 (mtp) cc_final: 0.9023 (mtp) REVERT: B 208 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: C 73 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8321 (tm-30) REVERT: D 46 GLN cc_start: 0.8243 (tp40) cc_final: 0.7845 (tp40) REVERT: D 48 ARG cc_start: 0.8263 (mtm180) cc_final: 0.7500 (ppt170) REVERT: D 67 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: D 73 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: D 98 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7311 (t70) REVERT: E 48 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7390 (ppt170) REVERT: E 164 ASP cc_start: 0.8276 (p0) cc_final: 0.8044 (p0) REVERT: F 48 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7263 (ppt170) REVERT: F 73 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: F 239 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8293 (pm20) outliers start: 39 outliers final: 21 residues processed: 169 average time/residue: 1.7117 time to fit residues: 314.6590 Evaluate side-chains 158 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 2.096 ------------------------------------------------------------------------------- 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 254 VAL 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 73 GLU 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 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 D residue 288 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16422 Z= 0.314 Angle : 0.526 5.528 22326 Z= 0.270 Chirality : 0.044 0.186 2520 Planarity : 0.004 0.038 2952 Dihedral : 5.005 83.219 2271 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.36 % Allowed : 16.96 % Favored : 80.67 % 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: -1.15 (0.46), residues: 126 sheet: -0.23 (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 A 173 HIS 0.002 0.001 HIS A 309 PHE 0.030 0.002 PHE E 214 TYR 0.012 0.002 TYR D 130 ARG 0.008 0.000 ARG D 314 *********************** 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: 40 poor density : 132 time to evaluate : 2.044 Fit side-chains REVERT: A 36 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: B 73 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8361 (tm-30) REVERT: B 151 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8885 (mtt) REVERT: B 208 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: C 73 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: D 46 GLN cc_start: 0.8296 (tp40) cc_final: 0.7901 (tp40) REVERT: D 48 ARG cc_start: 0.8297 (mtm180) cc_final: 0.7529 (ppt170) REVERT: D 67 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: D 73 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8315 (tm-30) REVERT: D 98 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7355 (t70) REVERT: E 48 ARG cc_start: 0.8250 (mtm180) cc_final: 0.7443 (ppt170) REVERT: E 73 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: E 164 ASP cc_start: 0.8317 (p0) cc_final: 0.8110 (p0) REVERT: E 208 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: F 48 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7457 (ppt170) REVERT: F 73 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: F 208 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: F 239 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8347 (pm20) outliers start: 40 outliers final: 20 residues processed: 169 average time/residue: 1.7774 time to fit residues: 329.5028 Evaluate side-chains 162 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 254 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.5980 chunk 118 optimal weight: 0.0770 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- 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 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16422 Z= 0.222 Angle : 0.494 7.018 22326 Z= 0.254 Chirality : 0.043 0.173 2520 Planarity : 0.004 0.038 2952 Dihedral : 4.812 82.664 2271 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.19 % Allowed : 17.20 % 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: -0.87 (0.17), residues: 2076 helix: -1.02 (0.47), residues: 126 sheet: -0.31 (0.16), residues: 924 loop : -0.64 (0.18), residues: 1026 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 D 130 ARG 0.006 0.000 ARG D 314 ********************** 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 165 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 1.903 Fit side-chains REVERT: A 36 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: B 73 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: B 151 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8879 (mtt) REVERT: B 203 MET cc_start: 0.9300 (mtp) cc_final: 0.9023 (mtp) REVERT: B 208 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: C 73 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: D 46 GLN cc_start: 0.8258 (tp40) cc_final: 0.7868 (tp40) REVERT: D 48 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7509 (ppt170) REVERT: D 67 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: D 73 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: D 98 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7365 (t70) REVERT: E 48 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7421 (ppt170) REVERT: E 73 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: E 164 ASP cc_start: 0.8282 (p0) cc_final: 0.8065 (p0) REVERT: E 208 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: F 48 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7292 (ppt170) REVERT: F 73 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: F 239 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8336 (pm20) outliers start: 37 outliers final: 22 residues processed: 160 average time/residue: 1.7047 time to fit residues: 296.5431 Evaluate side-chains 159 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.083301 restraints weight = 21495.723| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.12 r_work: 0.2809 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1775 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= 0.334 Angle : 0.541 6.259 22326 Z= 0.278 Chirality : 0.044 0.174 2520 Planarity : 0.004 0.040 2952 Dihedral : 5.072 81.829 2271 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.36 % Allowed : 17.20 % Favored : 80.44 % 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: -0.84 (0.17), residues: 2076 helix: -1.19 (0.46), residues: 126 sheet: -0.21 (0.16), residues: 900 loop : -0.69 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 173 HIS 0.002 0.001 HIS A 309 PHE 0.031 0.002 PHE E 214 TYR 0.012 0.002 TYR D 130 ARG 0.008 0.000 ARG D 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5543.58 seconds wall clock time: 100 minutes 49.08 seconds (6049.08 seconds total)