Starting phenix.real_space_refine on Sun Aug 24 01:16:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ed0_28026/08_2025/8ed0_28026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ed0_28026/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ed0_28026/08_2025/8ed0_28026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ed0_28026/08_2025/8ed0_28026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ed0_28026/08_2025/8ed0_28026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ed0_28026/08_2025/8ed0_28026.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16074 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "C" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "D" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "E" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "F" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Time building chain proxies: 3.90, per 1000 atoms: 0.24 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: 1.21 Conformation dependent library (CDL) restraints added in 734.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.52 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: 1.95 Time building geometry restraints manager: 1.69 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.940 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (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 ARG 0.009 0.001 ARG B 296 TYR 0.015 0.002 TYR C 337 PHE 0.016 0.002 PHE F 10 TRP 0.003 0.001 TRP D 173 HIS 0.009 0.002 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00671 (16422) covalent geometry : angle 0.75171 (22326) hydrogen bonds : bond 0.14517 ( 108) hydrogen bonds : angle 6.28054 ( 324) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 0.509 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: 0.8336 time to fit residues: 184.1153 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 : 0.635 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 A 344 HIS B 78 ASN B 344 HIS C 110 ASN C 344 HIS D 46 GLN D 110 ASN D 344 HIS E 110 ASN E 344 HIS F 110 ASN F 344 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.092824 restraints weight = 19183.519| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.07 r_work: 0.2938 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1407 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= 0.096 Angle : 0.480 4.706 22326 Z= 0.247 Chirality : 0.043 0.132 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.265 18.060 2269 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.36 % Allowed : 12.59 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.17), residues: 2076 helix: -1.96 (0.46), residues: 126 sheet: -0.53 (0.16), residues: 936 loop : -1.04 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 2 TYR 0.007 0.001 TYR B 192 PHE 0.023 0.001 PHE D 214 TRP 0.004 0.001 TRP D 173 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00210 (16422) covalent geometry : angle 0.47963 (22326) hydrogen bonds : bond 0.03420 ( 108) hydrogen bonds : angle 4.17763 ( 324) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.727 Fit side-chains REVERT: D 151 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8597 (mmm) REVERT: E 46 GLN cc_start: 0.8195 (tp40) cc_final: 0.7894 (tp40) REVERT: E 151 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.7472 (mmt) outliers start: 40 outliers final: 9 residues processed: 225 average time/residue: 0.8417 time to fit residues: 204.6625 Evaluate side-chains 191 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 289 LEU 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 151 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 66 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 4 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 134 optimal weight: 0.2980 chunk 99 optimal weight: 0.4980 chunk 143 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 50 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 46 GLN B 263 ASN C 57 GLN C 110 ASN E 110 ASN F 57 GLN F 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.090333 restraints weight = 19509.143| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.09 r_work: 0.2899 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1563 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= 0.132 Angle : 0.500 6.417 22326 Z= 0.251 Chirality : 0.043 0.135 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.294 18.483 2269 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.66 % Allowed : 12.77 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.18), residues: 2076 helix: -1.42 (0.48), residues: 126 sheet: -0.29 (0.17), residues: 936 loop : -0.68 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 2 TYR 0.008 0.001 TYR D 130 PHE 0.027 0.001 PHE F 214 TRP 0.004 0.001 TRP D 173 HIS 0.003 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00301 (16422) covalent geometry : angle 0.49967 (22326) hydrogen bonds : bond 0.03590 ( 108) hydrogen bonds : angle 4.04655 ( 324) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.586 Fit side-chains REVERT: A 2 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8200 (mtp180) REVERT: A 41 ARG cc_start: 0.8379 (mtt90) cc_final: 0.8037 (mpt180) REVERT: A 151 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: A 185 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 57 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: C 147 ARG cc_start: 0.8757 (mpt180) cc_final: 0.8487 (mpt180) REVERT: D 239 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: E 46 GLN cc_start: 0.8213 (tp40) cc_final: 0.7842 (tp40) REVERT: E 239 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8481 (pm20) outliers start: 45 outliers final: 16 residues processed: 216 average time/residue: 0.7259 time to fit residues: 170.0600 Evaluate side-chains 193 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 B residue 289 LEU Chi-restraints excluded: chain C residue 43 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 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 243 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 3 optimal weight: 0.2980 chunk 150 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 175 optimal weight: 0.0170 chunk 146 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 87 optimal weight: 0.3980 chunk 172 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 E 78 ASN F 46 GLN F 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.091457 restraints weight = 19626.244| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.10 r_work: 0.2941 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 16422 Z= 0.089 Angle : 0.452 6.692 22326 Z= 0.226 Chirality : 0.042 0.128 2520 Planarity : 0.004 0.039 2952 Dihedral : 3.963 18.123 2269 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 14.01 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.18), residues: 2076 helix: -1.05 (0.48), residues: 126 sheet: -0.23 (0.17), residues: 936 loop : -0.53 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 2 TYR 0.008 0.001 TYR E 192 PHE 0.029 0.001 PHE E 214 TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00197 (16422) covalent geometry : angle 0.45241 (22326) hydrogen bonds : bond 0.02779 ( 108) hydrogen bonds : angle 3.99233 ( 324) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.645 Fit side-chains REVERT: A 2 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8205 (mtp180) REVERT: A 151 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.7869 (mmt) REVERT: A 185 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8189 (mt-10) REVERT: B 57 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: C 147 ARG cc_start: 0.8557 (mpt180) cc_final: 0.8265 (mpt180) REVERT: D 151 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8538 (mmm) REVERT: E 151 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.7521 (mmt) REVERT: E 239 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: F 151 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7270 (mmt) outliers start: 36 outliers final: 15 residues processed: 217 average time/residue: 0.6219 time to fit residues: 147.1100 Evaluate side-chains 196 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 57 GLN 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 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 257 ILE 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 239 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 201 optimal weight: 0.5980 chunk 131 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 30 optimal weight: 0.0040 chunk 49 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 3.5198 ------------------------------------------------------------------------------- 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 F 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.097067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.085933 restraints weight = 19800.226| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.11 r_work: 0.2843 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16422 Z= 0.250 Angle : 0.582 8.385 22326 Z= 0.293 Chirality : 0.046 0.148 2520 Planarity : 0.005 0.040 2952 Dihedral : 4.729 22.688 2269 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.72 % Allowed : 14.24 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.18), residues: 2076 helix: -0.97 (0.49), residues: 126 sheet: -0.09 (0.17), residues: 912 loop : -0.49 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 2 TYR 0.014 0.002 TYR D 337 PHE 0.031 0.002 PHE F 214 TRP 0.004 0.001 TRP B 173 HIS 0.004 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00592 (16422) covalent geometry : angle 0.58246 (22326) hydrogen bonds : bond 0.04341 ( 108) hydrogen bonds : angle 4.27843 ( 324) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.626 Fit side-chains REVERT: A 185 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8125 (mt-10) REVERT: A 296 ARG cc_start: 0.7456 (ttt180) cc_final: 0.7221 (ttt180) REVERT: B 57 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: C 36 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: D 212 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: E 46 GLN cc_start: 0.8138 (tp40) cc_final: 0.7829 (tp40) REVERT: E 56 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7449 (mtp85) REVERT: E 212 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: E 239 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8575 (pm20) REVERT: E 296 ARG cc_start: 0.7585 (ttt180) cc_final: 0.7347 (ttt-90) REVERT: F 63 ASN cc_start: 0.8983 (p0) cc_final: 0.8624 (p0) REVERT: F 73 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: F 212 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7023 (mp0) outliers start: 46 outliers final: 17 residues processed: 201 average time/residue: 0.6825 time to fit residues: 148.9702 Evaluate side-chains 189 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 36 GLU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 130 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 46 GLN F 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.088634 restraints weight = 19456.389| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.09 r_work: 0.2869 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16422 Z= 0.147 Angle : 0.505 7.350 22326 Z= 0.253 Chirality : 0.043 0.136 2520 Planarity : 0.004 0.037 2952 Dihedral : 4.418 22.741 2269 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.84 % Allowed : 14.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.18), residues: 2076 helix: -0.82 (0.49), residues: 126 sheet: -0.14 (0.17), residues: 912 loop : -0.43 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 2 TYR 0.009 0.001 TYR D 130 PHE 0.031 0.002 PHE F 214 TRP 0.004 0.001 TRP C 173 HIS 0.002 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00337 (16422) covalent geometry : angle 0.50533 (22326) hydrogen bonds : bond 0.03549 ( 108) hydrogen bonds : angle 4.23156 ( 324) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.450 Fit side-chains REVERT: A 41 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7325 (mtt180) REVERT: A 151 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.7921 (mmt) REVERT: A 185 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 46 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7963 (mm-40) REVERT: B 57 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: E 46 GLN cc_start: 0.8125 (tp40) cc_final: 0.7833 (tp40) REVERT: E 56 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7317 (mtp85) REVERT: E 212 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: F 73 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: F 212 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6734 (mp0) outliers start: 48 outliers final: 21 residues processed: 209 average time/residue: 0.6415 time to fit residues: 146.0594 Evaluate side-chains 197 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 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 257 ILE 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 257 ILE Chi-restraints excluded: chain F residue 43 GLN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 chunk 138 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 195 optimal weight: 0.2980 chunk 159 optimal weight: 10.0000 overall best weight: 1.4622 ------------------------------------------------------------------------------- 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 F 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.089512 restraints weight = 19359.878| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.09 r_work: 0.2889 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1877 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= 0.127 Angle : 0.493 7.819 22326 Z= 0.246 Chirality : 0.043 0.139 2520 Planarity : 0.004 0.038 2952 Dihedral : 4.279 22.196 2269 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.60 % Allowed : 14.36 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.18), residues: 2076 helix: -0.72 (0.49), residues: 126 sheet: -0.25 (0.16), residues: 936 loop : -0.43 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 2 TYR 0.009 0.001 TYR B 130 PHE 0.010 0.001 PHE F 214 TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00288 (16422) covalent geometry : angle 0.49277 (22326) hydrogen bonds : bond 0.03222 ( 108) hydrogen bonds : angle 4.19830 ( 324) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.516 Fit side-chains REVERT: A 41 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7335 (mtt180) REVERT: A 151 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.7888 (mmt) REVERT: A 185 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 57 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: C 147 ARG cc_start: 0.8703 (mpt180) cc_final: 0.8449 (mpt180) REVERT: E 212 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: F 73 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: F 212 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.6755 (mp0) outliers start: 44 outliers final: 20 residues processed: 199 average time/residue: 0.7120 time to fit residues: 154.2502 Evaluate side-chains 195 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 B residue 57 GLN 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 15 ASP 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 257 ILE Chi-restraints excluded: chain E residue 292 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 203 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 0.0370 chunk 45 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.091016 restraints weight = 19567.308| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.10 r_work: 0.2933 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2147 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= 0.086 Angle : 0.456 7.957 22326 Z= 0.226 Chirality : 0.042 0.137 2520 Planarity : 0.004 0.038 2952 Dihedral : 3.966 27.792 2269 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.19 % Allowed : 14.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.18), residues: 2076 helix: -0.59 (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 ARG 0.009 0.000 ARG A 2 TYR 0.008 0.001 TYR B 192 PHE 0.032 0.001 PHE E 214 TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00190 (16422) covalent geometry : angle 0.45615 (22326) hydrogen bonds : bond 0.02582 ( 108) hydrogen bonds : angle 4.14947 ( 324) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.453 Fit side-chains REVERT: A 151 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.7878 (mmt) REVERT: A 185 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8204 (mt-10) REVERT: E 46 GLN cc_start: 0.8070 (tp40) cc_final: 0.7769 (mm110) REVERT: E 56 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7443 (mtp85) REVERT: F 73 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: F 151 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7497 (mmt) outliers start: 37 outliers final: 16 residues processed: 200 average time/residue: 0.6607 time to fit residues: 143.8092 Evaluate side-chains 190 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 190 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 215 ASP Chi-restraints excluded: chain D residue 257 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 200 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.3104 r_free = 0.3104 target = 0.098372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.087164 restraints weight = 19573.695| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.10 r_work: 0.2857 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16422 Z= 0.210 Angle : 0.564 9.264 22326 Z= 0.283 Chirality : 0.045 0.179 2520 Planarity : 0.004 0.040 2952 Dihedral : 4.651 27.130 2269 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 15.01 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.18), residues: 2076 helix: -0.67 (0.50), residues: 126 sheet: -0.10 (0.17), residues: 912 loop : -0.40 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 2 TYR 0.012 0.002 TYR D 337 PHE 0.027 0.002 PHE A 214 TRP 0.003 0.001 TRP B 173 HIS 0.003 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00492 (16422) covalent geometry : angle 0.56438 (22326) hydrogen bonds : bond 0.04084 ( 108) hydrogen bonds : angle 4.29974 ( 324) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.533 Fit side-chains REVERT: A 185 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8229 (mt-10) REVERT: E 46 GLN cc_start: 0.8119 (tp40) cc_final: 0.7803 (tp40) REVERT: E 56 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7470 (mtp85) REVERT: F 73 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8538 (tt0) outliers start: 32 outliers final: 15 residues processed: 183 average time/residue: 0.6530 time to fit residues: 129.9905 Evaluate side-chains 175 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 215 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 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 91 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3107 r_free = 0.3107 target = 0.098659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.087499 restraints weight = 19516.809| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.10 r_work: 0.2861 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- 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 0.036 16422 Z= 0.191 Angle : 0.546 8.748 22326 Z= 0.274 Chirality : 0.045 0.147 2520 Planarity : 0.005 0.040 2952 Dihedral : 4.620 27.783 2269 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.42 % Allowed : 15.48 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.18), residues: 2076 helix: -0.66 (0.50), residues: 126 sheet: -0.14 (0.17), residues: 912 loop : -0.41 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 2 TYR 0.010 0.002 TYR C 187 PHE 0.034 0.002 PHE E 214 TRP 0.003 0.001 TRP C 173 HIS 0.003 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00444 (16422) covalent geometry : angle 0.54560 (22326) hydrogen bonds : bond 0.03900 ( 108) hydrogen bonds : angle 4.32314 ( 324) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.664 Fit side-chains REVERT: A 41 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7331 (mtt180) REVERT: A 185 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8182 (mt-10) REVERT: C 36 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: E 46 GLN cc_start: 0.8144 (tp40) cc_final: 0.7807 (tp40) REVERT: E 56 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7461 (mtp85) REVERT: F 73 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: F 212 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7070 (mp0) outliers start: 24 outliers final: 18 residues processed: 177 average time/residue: 0.6933 time to fit residues: 132.9061 Evaluate side-chains 183 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 36 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 15 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 93 optimal weight: 0.0470 chunk 133 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.088315 restraints weight = 19361.021| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.09 r_work: 0.2866 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16422 Z= 0.179 Angle : 0.539 8.703 22326 Z= 0.271 Chirality : 0.044 0.153 2520 Planarity : 0.004 0.043 2952 Dihedral : 4.593 27.651 2269 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 15.19 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.18), residues: 2076 helix: -0.64 (0.50), residues: 126 sheet: -0.13 (0.17), residues: 912 loop : -0.43 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 2 TYR 0.010 0.002 TYR C 187 PHE 0.030 0.002 PHE F 214 TRP 0.003 0.001 TRP C 173 HIS 0.003 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00416 (16422) covalent geometry : angle 0.53936 (22326) hydrogen bonds : bond 0.03795 ( 108) hydrogen bonds : angle 4.29636 ( 324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4431.22 seconds wall clock time: 76 minutes 24.37 seconds (4584.37 seconds total)