Starting phenix.real_space_refine on Sat Jun 14 08:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ed0_28026/06_2025/8ed0_28026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ed0_28026/06_2025/8ed0_28026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ed0_28026/06_2025/8ed0_28026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ed0_28026/06_2025/8ed0_28026.map" model { file = "/net/cci-nas-00/data/ceres_data/8ed0_28026/06_2025/8ed0_28026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ed0_28026/06_2025/8ed0_28026.cif" } resolution = 2.72 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= 0.014 sd= 0.236 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 18 residue(s): 0.07s 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: 9.37, per 1000 atoms: 0.58 Number of scatterers: 16074 At special positions: 0 Unit cell: (113.1, 123.54, 102.66, 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: 3.81 Conformation dependent library (CDL) restraints added in 2.7 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: 29 helices and 12 sheets defined 8.8% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' 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 4 No H-bonds generated for 'chain 'B' and resid 2 through 4' 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 4 No H-bonds generated for 'chain 'C' and resid 2 through 4' 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 4 No H-bonds generated for 'chain 'D' and resid 2 through 4' 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 4 No H-bonds generated for 'chain 'E' and resid 2 through 4' 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 4 No H-bonds generated for 'chain 'F' and resid 2 through 4' 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 6 through 12 removed outlier: 4.236A 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 128 through 146 removed outlier: 6.405A pdb=" N ASP A 157 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 142 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN A 155 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 144 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.595A 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: 3.954A pdb=" N ASP A 238 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 12 removed outlier: 4.236A 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 128 through 146 removed outlier: 6.404A pdb=" N ASP B 157 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA B 142 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN B 155 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE B 144 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.595A 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: 3.954A pdb=" N ASP B 238 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 12 removed outlier: 4.235A 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 128 through 146 removed outlier: 6.405A pdb=" N ASP C 157 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA C 142 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN C 155 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C 144 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.596A 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: 3.954A pdb=" N ASP C 238 " --> pdb=" O ASN C 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 12 removed outlier: 4.236A 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 128 through 146 removed outlier: 6.405A pdb=" N ASP D 157 " --> pdb=" O ASN D 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 142 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN D 155 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE D 144 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.596A 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: 3.954A pdb=" N ASP D 238 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 12 removed outlier: 4.236A 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 128 through 146 removed outlier: 6.405A pdb=" N ASP E 157 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA E 142 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN E 155 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE E 144 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.596A 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: 3.953A pdb=" N ASP E 238 " --> pdb=" O ASN E 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 12 removed outlier: 4.237A 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 128 through 146 removed outlier: 6.405A pdb=" N ASP F 157 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA F 142 " --> pdb=" O ASN F 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN F 155 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE F 144 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.595A 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: 3.954A pdb=" N ASP F 238 " --> pdb=" O ASN F 223 " (cutoff:3.500A) 108 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: 4.54 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2749 1.31 - 1.43: 4328 1.43 - 1.56: 9279 1.56 - 1.68: 0 1.68 - 1.80: 66 Bond restraints: 16422 Sorted by residual: bond pdb=" CA TYR A 337 " pdb=" C TYR A 337 " ideal model delta sigma weight residual 1.522 1.475 0.047 9.30e-03 1.16e+04 2.58e+01 bond pdb=" CA TYR B 337 " pdb=" C TYR B 337 " ideal model delta sigma weight residual 1.522 1.475 0.047 9.30e-03 1.16e+04 2.55e+01 bond pdb=" CB ASP F 251 " pdb=" CG ASP F 251 " ideal model delta sigma weight residual 1.516 1.412 0.104 2.50e-02 1.60e+03 1.73e+01 bond pdb=" C TYR C 337 " pdb=" O TYR C 337 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.26e-02 6.30e+03 1.48e+01 bond pdb=" CA ASP F 251 " pdb=" C ASP F 251 " ideal model delta sigma weight residual 1.528 1.483 0.044 1.37e-02 5.33e+03 1.04e+01 ... (remaining 16417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 21639 1.83 - 3.65: 590 3.65 - 5.48: 74 5.48 - 7.31: 15 7.31 - 9.13: 8 Bond angle restraints: 22326 Sorted by residual: angle pdb=" N GLU D 338 " pdb=" CA GLU D 338 " pdb=" C GLU D 338 " ideal model delta sigma weight residual 110.97 117.70 -6.73 1.09e+00 8.42e-01 3.82e+01 angle pdb=" N ASP F 251 " pdb=" CA ASP F 251 " pdb=" C ASP F 251 " ideal model delta sigma weight residual 110.53 117.88 -7.35 1.29e+00 6.01e-01 3.24e+01 angle pdb=" N ASP D 251 " pdb=" CA ASP D 251 " pdb=" C ASP D 251 " ideal model delta sigma weight residual 110.41 117.28 -6.87 1.23e+00 6.61e-01 3.12e+01 angle pdb=" N GLU C 338 " pdb=" CA GLU C 338 " pdb=" C GLU C 338 " ideal model delta sigma weight residual 111.11 117.80 -6.69 1.20e+00 6.94e-01 3.11e+01 angle pdb=" N GLU F 338 " pdb=" CA GLU F 338 " pdb=" C GLU F 338 " ideal model delta sigma weight residual 111.03 117.11 -6.08 1.11e+00 8.12e-01 3.00e+01 ... (remaining 22321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8993 17.80 - 35.60: 505 35.60 - 53.40: 177 53.40 - 71.20: 30 71.20 - 89.00: 27 Dihedral angle restraints: 9732 sinusoidal: 3774 harmonic: 5958 Sorted by residual: dihedral pdb=" CA VAL E 254 " pdb=" C VAL E 254 " pdb=" N LYS E 255 " pdb=" CA LYS E 255 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C ARG E 56 " pdb=" N ARG E 56 " pdb=" CA ARG E 56 " pdb=" CB ARG E 56 " ideal model delta harmonic sigma weight residual -122.60 -113.33 -9.27 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" CA PHE F 74 " pdb=" C PHE F 74 " pdb=" N THR F 75 " pdb=" CA THR F 75 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2020 0.057 - 0.113: 398 0.113 - 0.170: 87 0.170 - 0.226: 7 0.226 - 0.283: 8 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA GLU C 338 " pdb=" N GLU C 338 " pdb=" C GLU C 338 " pdb=" CB GLU C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA GLU D 338 " pdb=" N GLU D 338 " pdb=" C GLU D 338 " pdb=" CB GLU D 338 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TYR B 337 " pdb=" N TYR B 337 " pdb=" C TYR B 337 " pdb=" CB TYR B 337 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2517 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 337 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C TYR A 337 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR A 337 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 338 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 337 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C TYR B 337 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR B 337 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 338 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 55 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C MET E 55 " 0.047 2.00e-02 2.50e+03 pdb=" O MET E 55 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG E 56 " -0.016 2.00e-02 2.50e+03 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1672 2.74 - 3.28: 15241 3.28 - 3.82: 27269 3.82 - 4.36: 36569 4.36 - 4.90: 59975 Nonbonded interactions: 140726 Sorted by model distance: nonbonded pdb=" NH2 ARG A 132 " pdb=" OE2 GLU C 276 " model vdw 2.201 3.120 nonbonded pdb=" OE2 GLU B 276 " pdb=" NH2 ARG C 132 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU D 276 " pdb=" NH2 ARG F 132 " model vdw 2.207 3.120 nonbonded pdb=" NH2 ARG D 132 " pdb=" OE2 GLU E 276 " model vdw 2.212 3.120 nonbonded pdb=" NH2 ARG E 132 " pdb=" OE2 GLU F 276 " model vdw 2.221 3.120 ... (remaining 140721 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: 0.13 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 35.550 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 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 : 0.007 0.104 16422 Z= 0.321 Angle : 0.752 9.132 22326 Z= 0.440 Chirality : 0.051 0.283 2520 Planarity : 0.006 0.042 2952 Dihedral : 14.421 89.003 5928 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.90 % Favored : 95.52 % Rotamer: Outliers : 0.18 % Allowed : 13.00 % Favored : 86.82 % Cbeta Deviations : 0.05 % 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: -2.14 (0.16), residues: 2076 helix: -3.07 (0.33), residues: 126 sheet: -0.77 (0.16), residues: 906 loop : -1.77 (0.15), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 173 HIS 0.009 0.002 HIS B 344 PHE 0.016 0.002 PHE F 10 TYR 0.015 0.002 TYR C 337 ARG 0.009 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.14517 ( 108) hydrogen bonds : angle 6.28054 ( 324) covalent geometry : bond 0.00671 (16422) covalent geometry : angle 0.75171 (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 206 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 1.963 Fit side-chains REVERT: B 296 ARG cc_start: 0.7334 (ttt180) cc_final: 0.7125 (ttt180) REVERT: B 324 ASP cc_start: 0.8481 (p0) cc_final: 0.8273 (p0) REVERT: C 36 GLU cc_start: 0.8275 (pp20) cc_final: 0.8009 (pp20) REVERT: D 17 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8166 (mmtp) REVERT: D 36 GLU cc_start: 0.8297 (pp20) cc_final: 0.8072 (pp20) REVERT: E 36 GLU cc_start: 0.8327 (pp20) cc_final: 0.8108 (pp20) REVERT: F 36 GLU cc_start: 0.8284 (pp20) cc_final: 0.8078 (pp20) REVERT: F 151 MET cc_start: 0.9005 (mmt) cc_final: 0.8672 (mmm) outliers start: 3 outliers final: 1 residues processed: 205 average time/residue: 1.7481 time to fit residues: 387.1947 Evaluate side-chains 164 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 66 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0470 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 110 ASN B 78 ASN B 344 HIS C 110 ASN D 46 GLN D 110 ASN D 344 HIS E 110 ASN E 344 HIS F 110 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.091000 restraints weight = 19304.335| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.08 r_work: 0.2909 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16422 Z= 0.117 Angle : 0.500 5.098 22326 Z= 0.257 Chirality : 0.044 0.133 2520 Planarity : 0.004 0.040 2952 Dihedral : 4.433 18.820 2269 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.66 % Allowed : 12.65 % Favored : 84.69 % 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 (0.17), residues: 2076 helix: -1.98 (0.46), residues: 126 sheet: -0.40 (0.16), residues: 912 loop : -1.03 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 173 HIS 0.003 0.001 HIS E 344 PHE 0.022 0.001 PHE D 214 TYR 0.008 0.001 TYR A 130 ARG 0.008 0.000 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 108) hydrogen bonds : angle 4.29969 ( 324) covalent geometry : bond 0.00262 (16422) covalent geometry : angle 0.49953 (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 236 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.911 Fit side-chains REVERT: C 57 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: E 46 GLN cc_start: 0.8184 (tp40) cc_final: 0.7856 (tp40) REVERT: E 151 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.7548 (mmt) outliers start: 45 outliers final: 17 residues processed: 218 average time/residue: 1.5603 time to fit residues: 369.7544 Evaluate side-chains 194 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 243 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 263 ASN C 110 ASN C 344 HIS D 46 GLN E 110 ASN F 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.087490 restraints weight = 19496.046| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.10 r_work: 0.2864 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16422 Z= 0.183 Angle : 0.542 6.756 22326 Z= 0.273 Chirality : 0.045 0.139 2520 Planarity : 0.004 0.040 2952 Dihedral : 4.595 21.753 2269 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.96 % Allowed : 12.77 % Favored : 84.28 % 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 (0.18), residues: 2076 helix: -1.51 (0.48), residues: 126 sheet: -0.18 (0.17), residues: 912 loop : -0.68 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 173 HIS 0.003 0.001 HIS F 220 PHE 0.027 0.002 PHE F 214 TYR 0.011 0.001 TYR D 337 ARG 0.007 0.001 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 108) hydrogen bonds : angle 4.20287 ( 324) covalent geometry : bond 0.00428 (16422) covalent geometry : angle 0.54219 (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 241 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 1.892 Fit side-chains REVERT: A 2 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8240 (mtp85) REVERT: A 151 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.7913 (mmt) REVERT: B 57 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: B 323 ARG cc_start: 0.8524 (mtt90) cc_final: 0.8283 (mtt180) REVERT: C 57 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: D 239 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8596 (pm20) REVERT: E 56 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7479 (mtp85) REVERT: E 239 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: F 212 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.6942 (mp0) outliers start: 50 outliers final: 20 residues processed: 220 average time/residue: 1.7821 time to fit residues: 425.8630 Evaluate side-chains 198 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 57 GLN 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 15 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 257 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 1 optimal weight: 0.0770 chunk 81 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 35 optimal weight: 0.0000 chunk 44 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 overall best weight: 0.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 344 HIS B 78 ASN C 78 ASN C 110 ASN D 46 GLN F 46 GLN F 57 GLN F 110 ASN F 344 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.090101 restraints weight = 19485.058| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.09 r_work: 0.2921 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 16422 Z= 0.098 Angle : 0.466 6.781 22326 Z= 0.233 Chirality : 0.042 0.128 2520 Planarity : 0.004 0.041 2952 Dihedral : 4.113 21.079 2269 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.66 % Allowed : 13.59 % Favored : 83.75 % 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: -0.77 (0.18), residues: 2076 helix: -1.09 (0.49), residues: 126 sheet: -0.27 (0.17), residues: 936 loop : -0.53 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.002 0.001 HIS B 220 PHE 0.029 0.001 PHE E 214 TYR 0.008 0.001 TYR B 192 ARG 0.007 0.000 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 108) hydrogen bonds : angle 4.05716 ( 324) covalent geometry : bond 0.00217 (16422) covalent geometry : angle 0.46602 (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 237 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 1.836 Fit side-chains REVERT: A 151 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.7859 (mmt) REVERT: A 185 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8164 (mt-10) REVERT: B 57 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: D 151 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8537 (mmm) REVERT: D 327 VAL cc_start: 0.9297 (t) cc_final: 0.9091 (p) REVERT: E 46 GLN cc_start: 0.8092 (tp40) cc_final: 0.7833 (tp40) REVERT: E 239 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: F 151 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.7342 (mmt) outliers start: 45 outliers final: 19 residues processed: 219 average time/residue: 1.6335 time to fit residues: 388.6737 Evaluate side-chains 198 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain C residue 46 GLN 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 66 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 257 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 163 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 65 optimal weight: 0.0470 chunk 59 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 78 ASN C 110 ASN D 46 GLN F 46 GLN F 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.087144 restraints weight = 19622.742| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.10 r_work: 0.2846 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 16422 Z= 0.241 Angle : 0.581 8.582 22326 Z= 0.292 Chirality : 0.046 0.148 2520 Planarity : 0.005 0.040 2952 Dihedral : 4.769 23.211 2269 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.90 % Allowed : 13.53 % Favored : 83.57 % 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: -0.60 (0.18), residues: 2076 helix: -1.01 (0.49), residues: 126 sheet: -0.09 (0.17), residues: 912 loop : -0.50 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.003 0.001 HIS F 344 PHE 0.030 0.002 PHE F 214 TYR 0.013 0.002 TYR A 337 ARG 0.007 0.001 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 108) hydrogen bonds : angle 4.32652 ( 324) covalent geometry : bond 0.00567 (16422) covalent geometry : angle 0.58107 (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 218 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 1.803 Fit side-chains REVERT: A 41 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7290 (mtt180) REVERT: A 185 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8119 (mt-10) REVERT: B 46 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7915 (mm110) REVERT: B 57 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: D 212 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: E 56 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7492 (mtp85) REVERT: E 212 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: E 296 ARG cc_start: 0.7581 (ttt180) cc_final: 0.7341 (ttt-90) REVERT: F 212 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7099 (mp0) outliers start: 49 outliers final: 22 residues processed: 202 average time/residue: 1.6317 time to fit residues: 358.2376 Evaluate side-chains 190 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 66 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 C residue 339 THR Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 7 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 188 optimal weight: 0.0570 chunk 19 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 0.0040 chunk 24 optimal weight: 3.9990 overall best weight: 0.9912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 110 ASN B 78 ASN C 78 ASN C 110 ASN D 46 GLN E 42 GLN E 110 ASN F 110 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.091594 restraints weight = 19194.010| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.09 r_work: 0.2903 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16422 Z= 0.100 Angle : 0.468 7.568 22326 Z= 0.233 Chirality : 0.042 0.132 2520 Planarity : 0.004 0.038 2952 Dihedral : 4.160 30.338 2269 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.66 % Allowed : 14.18 % Favored : 83.16 % 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: -0.60 (0.18), residues: 2076 helix: -0.80 (0.49), residues: 126 sheet: -0.15 (0.17), residues: 924 loop : -0.44 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.002 0.001 HIS B 220 PHE 0.030 0.001 PHE F 214 TYR 0.008 0.001 TYR E 192 ARG 0.009 0.000 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 108) hydrogen bonds : angle 4.15505 ( 324) covalent geometry : bond 0.00223 (16422) covalent geometry : angle 0.46817 (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 225 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 1.941 Fit side-chains REVERT: A 151 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7912 (mmt) REVERT: A 185 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 57 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: D 327 VAL cc_start: 0.9290 (t) cc_final: 0.9076 (p) REVERT: E 46 GLN cc_start: 0.8115 (tp40) cc_final: 0.7834 (tp40) outliers start: 45 outliers final: 18 residues processed: 209 average time/residue: 1.4944 time to fit residues: 341.0923 Evaluate side-chains 187 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 257 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 41 optimal weight: 4.9990 chunk 198 optimal weight: 0.0870 chunk 93 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 65 optimal weight: 0.0040 chunk 42 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 overall best weight: 1.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.090964 restraints weight = 19367.585| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.10 r_work: 0.2905 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1944 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= 0.112 Angle : 0.481 8.273 22326 Z= 0.239 Chirality : 0.042 0.143 2520 Planarity : 0.004 0.037 2952 Dihedral : 4.146 27.889 2269 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.01 % Allowed : 14.83 % Favored : 83.16 % 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: -0.58 (0.18), residues: 2076 helix: -0.66 (0.50), residues: 126 sheet: -0.20 (0.17), residues: 936 loop : -0.39 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS B 220 PHE 0.009 0.001 PHE F 214 TYR 0.010 0.001 TYR C 187 ARG 0.008 0.000 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 108) hydrogen bonds : angle 4.15979 ( 324) covalent geometry : bond 0.00253 (16422) covalent geometry : angle 0.48059 (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 209 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 1.625 Fit side-chains REVERT: A 185 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8196 (mt-10) REVERT: B 57 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: D 327 VAL cc_start: 0.9288 (t) cc_final: 0.9066 (p) REVERT: E 46 GLN cc_start: 0.8098 (tp40) cc_final: 0.7822 (tp40) REVERT: E 212 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: F 73 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: F 212 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.6385 (mp0) outliers start: 34 outliers final: 19 residues processed: 194 average time/residue: 1.6172 time to fit residues: 342.0467 Evaluate side-chains 192 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 257 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 177 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0050 chunk 141 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 64 optimal weight: 0.0030 chunk 120 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.9808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 78 ASN C 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.089315 restraints weight = 19361.445| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.12 r_work: 0.2875 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16422 Z= 0.155 Angle : 0.514 8.487 22326 Z= 0.256 Chirality : 0.044 0.148 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.374 27.348 2269 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.66 % Allowed : 14.18 % Favored : 83.16 % 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: -0.49 (0.18), residues: 2076 helix: -0.64 (0.50), residues: 126 sheet: -0.11 (0.17), residues: 912 loop : -0.35 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.003 0.001 HIS F 220 PHE 0.031 0.002 PHE E 214 TYR 0.010 0.001 TYR D 337 ARG 0.009 0.000 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 108) hydrogen bonds : angle 4.23814 ( 324) covalent geometry : bond 0.00357 (16422) covalent geometry : angle 0.51378 (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 213 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.929 Fit side-chains REVERT: A 41 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7352 (mtt180) REVERT: A 185 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8240 (mt-10) REVERT: B 57 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: D 327 VAL cc_start: 0.9317 (t) cc_final: 0.9108 (p) REVERT: E 46 GLN cc_start: 0.8161 (tp40) cc_final: 0.7873 (tp40) REVERT: E 212 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: F 212 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7119 (mp0) outliers start: 45 outliers final: 22 residues processed: 197 average time/residue: 1.6065 time to fit residues: 345.9172 Evaluate side-chains 194 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 257 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 134 optimal weight: 0.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.090129 restraints weight = 19253.891| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.09 r_work: 0.2893 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16422 Z= 0.129 Angle : 0.495 8.388 22326 Z= 0.246 Chirality : 0.043 0.170 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.261 26.881 2269 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.89 % Allowed : 14.83 % Favored : 83.27 % 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: -0.47 (0.18), residues: 2076 helix: -0.60 (0.50), residues: 126 sheet: -0.11 (0.17), residues: 912 loop : -0.32 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS F 220 PHE 0.010 0.001 PHE D 7 TYR 0.009 0.001 TYR E 192 ARG 0.009 0.000 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 108) hydrogen bonds : angle 4.21029 ( 324) covalent geometry : bond 0.00295 (16422) covalent geometry : angle 0.49457 (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 202 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.709 Fit side-chains REVERT: A 41 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7304 (mtt180) REVERT: A 185 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 57 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: D 327 VAL cc_start: 0.9290 (t) cc_final: 0.9060 (p) REVERT: E 46 GLN cc_start: 0.8117 (tp40) cc_final: 0.7806 (tp40) REVERT: E 212 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: F 212 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.6459 (mp0) outliers start: 32 outliers final: 23 residues processed: 190 average time/residue: 1.8138 time to fit residues: 376.0872 Evaluate side-chains 193 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 257 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 141 optimal weight: 0.0770 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN B 78 ASN C 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.088479 restraints weight = 19546.923| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.10 r_work: 0.2866 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16422 Z= 0.177 Angle : 0.536 9.085 22326 Z= 0.268 Chirality : 0.044 0.154 2520 Planarity : 0.004 0.041 2952 Dihedral : 4.522 26.448 2269 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.95 % Allowed : 14.89 % Favored : 83.16 % 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: -0.50 (0.18), residues: 2076 helix: -0.66 (0.50), residues: 126 sheet: -0.11 (0.17), residues: 912 loop : -0.36 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.003 0.001 HIS F 220 PHE 0.035 0.002 PHE E 214 TYR 0.012 0.002 TYR D 337 ARG 0.009 0.000 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 108) hydrogen bonds : angle 4.28387 ( 324) covalent geometry : bond 0.00410 (16422) covalent geometry : angle 0.53600 (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 200 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.625 Fit side-chains REVERT: A 41 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7314 (mtt180) REVERT: A 185 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 46 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7903 (mm110) REVERT: B 57 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: E 46 GLN cc_start: 0.8132 (tp40) cc_final: 0.7809 (tp40) REVERT: E 212 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: F 63 ASN cc_start: 0.8869 (p0) cc_final: 0.8585 (p0) REVERT: F 212 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7105 (mp0) outliers start: 33 outliers final: 23 residues processed: 184 average time/residue: 1.5889 time to fit residues: 318.9098 Evaluate side-chains 194 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 257 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 181 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 2 optimal weight: 0.0270 chunk 161 optimal weight: 0.0470 chunk 82 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 152 optimal weight: 0.0970 chunk 50 optimal weight: 9.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN B 78 ASN C 13 GLN C 110 ASN F 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.090993 restraints weight = 19851.860| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.12 r_work: 0.2930 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16422 Z= 0.085 Angle : 0.457 8.125 22326 Z= 0.227 Chirality : 0.042 0.138 2520 Planarity : 0.004 0.039 2952 Dihedral : 3.944 26.187 2269 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.42 % Allowed : 15.72 % Favored : 82.86 % 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: -0.51 (0.18), residues: 2076 helix: -0.54 (0.49), residues: 126 sheet: -0.17 (0.17), residues: 936 loop : -0.34 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS C 309 PHE 0.008 0.001 PHE F 214 TYR 0.008 0.001 TYR E 192 ARG 0.009 0.000 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.02456 ( 108) hydrogen bonds : angle 4.17726 ( 324) covalent geometry : bond 0.00185 (16422) covalent geometry : angle 0.45697 (22326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10764.91 seconds wall clock time: 189 minutes 8.85 seconds (11348.85 seconds total)