Starting phenix.real_space_refine on Tue Dec 31 14:29:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ed0_28026/12_2024/8ed0_28026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ed0_28026/12_2024/8ed0_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_28026/12_2024/8ed0_28026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ed0_28026/12_2024/8ed0_28026.map" model { file = "/net/cci-nas-00/data/ceres_data/8ed0_28026/12_2024/8ed0_28026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ed0_28026/12_2024/8ed0_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): 0.05s 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: 9.51, per 1000 atoms: 0.59 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: 3.99 Conformation dependent library (CDL) restraints added in 2.2 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: 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: 1.59 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: 4.95 Time building geometry restraints manager: 4.47 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: 0.00 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: 2.250 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.350 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.060 ------------------------------------------------------------------------------- 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= 0.447 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 *********************** 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 : 1.786 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: 1.7977 time to fit residues: 399.1889 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 : 1.857 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 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= 0.175 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 *********************** 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 : 1.737 Fit side-chains REVERT: B 147 ARG cc_start: 0.8756 (mpt180) cc_final: 0.8554 (mpt180) REVERT: C 36 GLU cc_start: 0.8092 (pp20) cc_final: 0.7832 (pp20) REVERT: C 57 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: C 187 TYR cc_start: 0.8505 (m-80) cc_final: 0.8290 (m-80) REVERT: D 36 GLU cc_start: 0.8179 (pp20) cc_final: 0.7953 (pp20) REVERT: E 46 GLN cc_start: 0.8169 (tp40) cc_final: 0.7846 (tp40) REVERT: E 151 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.7679 (mmt) outliers start: 45 outliers final: 17 residues processed: 218 average time/residue: 1.6224 time to fit residues: 384.7500 Evaluate side-chains 196 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 102 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 0.0770 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 148 optimal weight: 0.4980 overall best weight: 1.0940 ------------------------------------------------------------------------------- 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 263 ASN C 110 ASN D 46 GLN E 110 ASN F 110 ASN F 344 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1606 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= 0.161 Angle : 0.477 6.254 22326 Z= 0.239 Chirality : 0.043 0.133 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.137 18.665 2269 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.90 % Allowed : 12.77 % Favored : 84.34 % 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: -0.88 (0.18), residues: 2076 helix: -1.40 (0.48), residues: 126 sheet: -0.28 (0.17), residues: 936 loop : -0.66 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.003 0.001 HIS F 220 PHE 0.026 0.001 PHE F 214 TYR 0.008 0.001 TYR E 192 ARG 0.007 0.000 ARG A 2 *********************** 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 250 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 1.983 Fit side-chains REVERT: A 41 ARG cc_start: 0.8308 (mtt90) cc_final: 0.8084 (mpt180) REVERT: A 151 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.7994 (mmt) REVERT: A 185 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 57 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: B 147 ARG cc_start: 0.8712 (mpt180) cc_final: 0.8443 (mpt180) REVERT: C 147 ARG cc_start: 0.8728 (mpt180) cc_final: 0.8430 (mpt180) REVERT: D 36 GLU cc_start: 0.8194 (pp20) cc_final: 0.7967 (pp20) REVERT: D 151 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8595 (mmm) REVERT: D 239 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: E 46 GLN cc_start: 0.8196 (tp40) cc_final: 0.7836 (tp40) REVERT: E 151 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.7648 (mmt) REVERT: E 239 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8462 (pm20) REVERT: F 151 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.7468 (mmt) outliers start: 49 outliers final: 16 residues processed: 230 average time/residue: 1.7058 time to fit residues: 426.9090 Evaluate side-chains 195 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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 339 THR Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain D residue 15 ASP 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 D residue 239 GLU Chi-restraints excluded: chain E residue 15 ASP 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 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 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 183 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 197 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 overall best weight: 3.3684 ------------------------------------------------------------------------------- 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 C 344 HIS D 46 GLN F 46 GLN F 57 GLN F 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16422 Z= 0.373 Angle : 0.582 8.168 22326 Z= 0.293 Chirality : 0.046 0.148 2520 Planarity : 0.005 0.042 2952 Dihedral : 4.790 23.265 2269 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.13 % Allowed : 13.12 % 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: -0.68 (0.18), residues: 2076 helix: -1.20 (0.48), residues: 126 sheet: -0.12 (0.17), residues: 912 loop : -0.56 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 173 HIS 0.004 0.001 HIS E 220 PHE 0.030 0.002 PHE E 214 TYR 0.015 0.002 TYR D 337 ARG 0.004 0.001 ARG A 56 *********************** 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 219 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 1.943 Fit side-chains REVERT: A 185 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7950 (mt-10) REVERT: D 36 GLU cc_start: 0.8262 (pp20) cc_final: 0.7998 (pp20) REVERT: D 212 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: E 212 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: E 239 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: F 212 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7134 (mp0) outliers start: 53 outliers final: 22 residues processed: 201 average time/residue: 1.6040 time to fit residues: 351.0270 Evaluate side-chains 189 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 66 VAL Chi-restraints excluded: chain B residue 190 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 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 212 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 168 optimal weight: 0.0050 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- 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 F 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 16422 Z= 0.467 Angle : 0.625 8.218 22326 Z= 0.316 Chirality : 0.048 0.157 2520 Planarity : 0.005 0.047 2952 Dihedral : 5.031 23.687 2269 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.25 % Allowed : 13.24 % Favored : 83.51 % 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: -0.70 (0.18), residues: 2076 helix: -1.12 (0.48), residues: 126 sheet: -0.13 (0.16), residues: 912 loop : -0.58 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 173 HIS 0.004 0.002 HIS F 344 PHE 0.018 0.002 PHE D 7 TYR 0.015 0.002 TYR D 337 ARG 0.004 0.001 ARG A 56 *********************** 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 212 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 157 time to evaluate : 1.846 Fit side-chains REVERT: A 41 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7251 (mtt180) REVERT: A 185 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 212 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: D 36 GLU cc_start: 0.8291 (pp20) cc_final: 0.8049 (pp20) REVERT: D 212 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: D 215 ASP cc_start: 0.8230 (m-30) cc_final: 0.8024 (m-30) REVERT: E 212 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: F 212 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7007 (mp0) outliers start: 55 outliers final: 27 residues processed: 195 average time/residue: 1.6648 time to fit residues: 353.1502 Evaluate side-chains 184 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 66 VAL 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 A residue 339 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 212 GLU 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 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 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 66 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 0.0770 chunk 65 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- 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 C 78 ASN C 110 ASN E 78 ASN F 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16422 Z= 0.198 Angle : 0.498 7.523 22326 Z= 0.249 Chirality : 0.043 0.129 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.407 19.475 2269 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.25 % Allowed : 13.36 % Favored : 83.39 % 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: -0.59 (0.18), residues: 2076 helix: -0.89 (0.49), residues: 126 sheet: -0.12 (0.17), residues: 912 loop : -0.45 (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 0.032 0.002 PHE D 214 TYR 0.009 0.001 TYR B 130 ARG 0.004 0.000 ARG D 296 *********************** 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 233 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 1.862 Fit side-chains REVERT: A 41 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7397 (mtt180) REVERT: A 151 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8052 (mmt) REVERT: A 185 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7952 (mt-10) REVERT: B 57 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: C 147 ARG cc_start: 0.8734 (mpt180) cc_final: 0.8447 (mpt180) REVERT: D 36 GLU cc_start: 0.8242 (pp20) cc_final: 0.7979 (pp20) REVERT: E 46 GLN cc_start: 0.8142 (tp40) cc_final: 0.7831 (tp40) REVERT: F 212 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.6588 (mp0) outliers start: 55 outliers final: 24 residues processed: 212 average time/residue: 1.6325 time to fit residues: 378.9962 Evaluate side-chains 193 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG 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 A residue 313 VAL 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 B residue 289 LEU Chi-restraints excluded: chain C residue 46 GLN 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 313 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 E residue 15 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 0.0270 chunk 110 optimal weight: 0.2980 chunk 196 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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 C 78 ASN C 110 ASN D 46 GLN E 42 GLN F 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16422 Z= 0.126 Angle : 0.458 7.939 22326 Z= 0.227 Chirality : 0.042 0.146 2520 Planarity : 0.004 0.034 2952 Dihedral : 3.971 27.040 2269 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.07 % Allowed : 14.42 % Favored : 83.51 % 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: -0.59 (0.18), residues: 2076 helix: -0.69 (0.49), residues: 126 sheet: -0.19 (0.16), residues: 936 loop : -0.40 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.002 0.000 HIS B 309 PHE 0.028 0.001 PHE F 214 TYR 0.009 0.001 TYR B 192 ARG 0.005 0.000 ARG D 296 *********************** 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 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 1.951 Fit side-chains REVERT: A 151 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.7972 (mmt) REVERT: A 185 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7993 (mt-10) REVERT: B 147 ARG cc_start: 0.8600 (mpt180) cc_final: 0.8317 (mpt180) REVERT: C 290 GLU cc_start: 0.8372 (tt0) cc_final: 0.8104 (mm-30) REVERT: D 36 GLU cc_start: 0.8204 (pp20) cc_final: 0.7938 (pp20) REVERT: D 147 ARG cc_start: 0.8510 (mpt180) cc_final: 0.8301 (mpt180) REVERT: D 327 VAL cc_start: 0.9224 (t) cc_final: 0.8963 (p) REVERT: E 46 GLN cc_start: 0.8085 (tp40) cc_final: 0.7812 (tp40) REVERT: F 73 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: F 151 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.7644 (mmt) outliers start: 35 outliers final: 18 residues processed: 205 average time/residue: 1.5863 time to fit residues: 355.0955 Evaluate side-chains 188 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 46 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 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 257 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 GLU 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 257 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 0.0670 chunk 154 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 42 GLN B 78 ASN C 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16422 Z= 0.271 Angle : 0.534 8.580 22326 Z= 0.266 Chirality : 0.044 0.158 2520 Planarity : 0.004 0.038 2952 Dihedral : 4.466 25.442 2269 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.72 % Allowed : 14.30 % Favored : 82.98 % 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: -0.48 (0.18), residues: 2076 helix: -0.67 (0.50), residues: 126 sheet: -0.06 (0.17), residues: 912 loop : -0.38 (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 344 PHE 0.032 0.002 PHE E 214 TYR 0.011 0.001 TYR E 192 ARG 0.006 0.000 ARG D 296 *********************** 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 215 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 2.182 Fit side-chains REVERT: A 41 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7415 (mtt180) REVERT: A 46 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8010 (mm-40) REVERT: A 151 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.7948 (mmt) REVERT: A 185 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7977 (mt-10) REVERT: B 46 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7974 (mm-40) REVERT: B 57 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7633 (mp10) REVERT: D 73 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8395 (tp30) REVERT: D 327 VAL cc_start: 0.9251 (t) cc_final: 0.8996 (p) REVERT: E 212 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: F 73 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: F 212 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7110 (mp0) outliers start: 46 outliers final: 20 residues processed: 202 average time/residue: 1.5731 time to fit residues: 346.9600 Evaluate side-chains 195 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 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 254 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 GLU 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 257 ILE 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 257 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 78 ASN C 110 ASN E 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16422 Z= 0.161 Angle : 0.483 8.153 22326 Z= 0.241 Chirality : 0.043 0.167 2520 Planarity : 0.004 0.034 2952 Dihedral : 4.150 25.141 2269 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.77 % Allowed : 15.48 % Favored : 82.74 % 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: -0.54 (0.18), residues: 2076 helix: -0.58 (0.50), residues: 126 sheet: -0.16 (0.17), residues: 936 loop : -0.38 (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 0.031 0.001 PHE A 214 TYR 0.009 0.001 TYR E 192 ARG 0.005 0.000 ARG D 296 *********************** 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: 30 poor density : 172 time to evaluate : 1.576 Fit side-chains REVERT: A 151 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.7968 (mmt) REVERT: A 185 GLU cc_start: 0.8225 (mt-10) cc_final: 0.8018 (mt-10) REVERT: D 36 GLU cc_start: 0.8217 (pp20) cc_final: 0.7929 (pp20) REVERT: D 327 VAL cc_start: 0.9224 (t) cc_final: 0.8964 (p) REVERT: E 46 GLN cc_start: 0.8137 (tp40) cc_final: 0.7807 (tp40) REVERT: E 212 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: F 73 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8464 (tt0) outliers start: 30 outliers final: 17 residues processed: 194 average time/residue: 1.5777 time to fit residues: 337.8447 Evaluate side-chains 184 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 313 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 46 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 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 257 ILE 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 239 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 193 optimal weight: 8.9990 chunk 118 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 0.0570 chunk 203 optimal weight: 8.9990 chunk 187 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 13 GLN C 110 ASN F 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 16422 Z= 0.114 Angle : 0.453 8.123 22326 Z= 0.224 Chirality : 0.042 0.142 2520 Planarity : 0.004 0.032 2952 Dihedral : 3.801 23.686 2269 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.00 % Allowed : 16.49 % Favored : 82.51 % 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: -0.48 (0.49), residues: 126 sheet: -0.12 (0.17), residues: 936 loop : -0.34 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 173 HIS 0.001 0.000 HIS B 220 PHE 0.037 0.001 PHE E 214 TYR 0.009 0.001 TYR E 192 ARG 0.002 0.000 ARG D 296 ********************** 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 188 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.726 Fit side-chains REVERT: A 185 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8006 (mt-10) REVERT: D 327 VAL cc_start: 0.9199 (t) cc_final: 0.8962 (p) REVERT: E 46 GLN cc_start: 0.8093 (tp40) cc_final: 0.7796 (mm110) REVERT: E 347 LYS cc_start: 0.8223 (ttmm) cc_final: 0.8020 (pttp) REVERT: F 53 MET cc_start: 0.8319 (ptt) cc_final: 0.8080 (ptp) REVERT: F 73 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: F 239 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8375 (pm20) outliers start: 17 outliers final: 12 residues processed: 184 average time/residue: 1.6399 time to fit residues: 328.2775 Evaluate side-chains 173 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain C residue 46 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 E residue 63 ASN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 239 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 172 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 13 GLN C 110 ASN F 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.084565 restraints weight = 19631.183| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.12 r_work: 0.2798 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 16422 Z= 0.670 Angle : 0.735 10.360 22326 Z= 0.372 Chirality : 0.053 0.182 2520 Planarity : 0.006 0.045 2952 Dihedral : 5.273 23.963 2269 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.01 % Allowed : 15.54 % Favored : 82.45 % 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: -0.56 (0.18), residues: 2076 helix: -0.91 (0.48), residues: 126 sheet: -0.02 (0.17), residues: 912 loop : -0.52 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 173 HIS 0.005 0.002 HIS D 90 PHE 0.025 0.003 PHE D 7 TYR 0.021 0.003 TYR A 337 ARG 0.009 0.001 ARG F 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5936.69 seconds wall clock time: 107 minutes 15.14 seconds (6435.14 seconds total)