Starting phenix.real_space_refine on Fri Feb 16 17:50:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/02_2024/8ed0_28026.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/02_2024/8ed0_28026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/02_2024/8ed0_28026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/02_2024/8ed0_28026.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/02_2024/8ed0_28026.pdb" } 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 Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.35, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 5.70 Conformation dependent library (CDL) restraints added in 3.1 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: 1.66 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: 4.36 Time building geometry restraints manager: 6.26 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: 99.51 - 106.41: 478 106.41 - 113.30: 8786 113.30 - 120.20: 5681 120.20 - 127.10: 7231 127.10 - 133.99: 150 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 2.520 nonbonded pdb=" OE2 GLU B 276 " pdb=" NH2 ARG C 132 " model vdw 2.202 2.520 nonbonded pdb=" OE2 GLU D 276 " pdb=" NH2 ARG F 132 " model vdw 2.207 2.520 nonbonded pdb=" NH2 ARG D 132 " pdb=" OE2 GLU E 276 " model vdw 2.212 2.520 nonbonded pdb=" NH2 ARG E 132 " pdb=" OE2 GLU F 276 " model vdw 2.221 2.520 ... (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 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.540 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 42.020 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.090 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 1.790 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: 1.6746 time to fit residues: 372.3677 Evaluate side-chains 164 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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: 7.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 104 optimal weight: 0.0060 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 overall best weight: 2.1800 ------------------------------------------------------------------------------- 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 110 ASN D 46 GLN D 110 ASN E 110 ASN F 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1112 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= 0.261 Angle : 0.531 5.824 22326 Z= 0.274 Chirality : 0.044 0.135 2520 Planarity : 0.004 0.040 2952 Dihedral : 4.684 20.248 2269 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.01 % Allowed : 11.52 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2076 helix: -2.05 (0.45), residues: 126 sheet: -0.28 (0.16), residues: 912 loop : -1.04 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 173 HIS 0.004 0.001 HIS E 344 PHE 0.025 0.002 PHE E 214 TYR 0.010 0.001 TYR A 337 ARG 0.007 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 229 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 178 time to evaluate : 1.812 Fit side-chains REVERT: B 50 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7858 (mt) REVERT: B 324 ASP cc_start: 0.8458 (p0) cc_final: 0.8255 (p0) REVERT: C 36 GLU cc_start: 0.8240 (pp20) cc_final: 0.8002 (pp20) REVERT: C 57 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: D 36 GLU cc_start: 0.8275 (pp20) cc_final: 0.8049 (pp20) REVERT: D 67 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: F 212 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6943 (mp0) outliers start: 51 outliers final: 19 residues processed: 212 average time/residue: 1.4768 time to fit residues: 342.8601 Evaluate side-chains 193 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 VAL 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 46 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 67 GLU 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 205 ASP Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 148 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 B 344 HIS C 78 ASN C 110 ASN D 344 HIS E 110 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16422 Z= 0.280 Angle : 0.528 5.690 22326 Z= 0.268 Chirality : 0.044 0.135 2520 Planarity : 0.004 0.040 2952 Dihedral : 4.625 23.144 2269 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.43 % Allowed : 12.47 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2076 helix: -1.52 (0.48), residues: 126 sheet: -0.02 (0.17), residues: 912 loop : -0.71 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.003 0.001 HIS E 344 PHE 0.011 0.002 PHE D 7 TYR 0.012 0.001 TYR D 337 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 237 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 179 time to evaluate : 2.046 Fit side-chains REVERT: A 185 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7928 (mt-10) REVERT: A 212 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: B 212 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: C 36 GLU cc_start: 0.8223 (pp20) cc_final: 0.7968 (pp20) REVERT: C 57 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: D 67 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: D 212 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: E 212 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: F 212 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6970 (mp0) outliers start: 58 outliers final: 27 residues processed: 220 average time/residue: 1.5495 time to fit residues: 371.6891 Evaluate side-chains 204 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 46 GLN 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 B residue 289 LEU Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 63 ASN 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 66 VAL Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 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 254 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN B 78 ASN C 78 ASN C 110 ASN C 344 HIS F 57 GLN F 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1473 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= 0.383 Angle : 0.576 6.425 22326 Z= 0.292 Chirality : 0.046 0.148 2520 Planarity : 0.005 0.043 2952 Dihedral : 4.849 23.436 2269 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.08 % Allowed : 12.35 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2076 helix: -1.30 (0.48), residues: 126 sheet: 0.06 (0.17), residues: 912 loop : -0.63 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 173 HIS 0.004 0.001 HIS E 344 PHE 0.030 0.002 PHE E 214 TYR 0.014 0.002 TYR E 337 ARG 0.003 0.000 ARG F 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 173 time to evaluate : 1.755 Fit side-chains REVERT: A 41 ARG cc_start: 0.8316 (mtt90) cc_final: 0.8008 (mpt180) REVERT: A 185 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 212 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 212 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: B 316 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: C 36 GLU cc_start: 0.8257 (pp20) cc_final: 0.8002 (pp20) REVERT: C 57 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: C 212 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: C 292 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9181 (mm) REVERT: C 316 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: D 67 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: D 212 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: E 212 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: F 212 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: F 316 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7456 (mp0) outliers start: 69 outliers final: 30 residues processed: 221 average time/residue: 1.5718 time to fit residues: 378.1562 Evaluate side-chains 206 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 46 GLN 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 239 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 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 254 VAL Chi-restraints excluded: chain F residue 316 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 chunk 146 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 42 GLN F 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 16422 Z= 0.297 Angle : 0.533 5.867 22326 Z= 0.270 Chirality : 0.044 0.139 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.673 20.500 2269 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.55 % Allowed : 13.12 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2076 helix: -1.05 (0.49), residues: 126 sheet: 0.10 (0.17), residues: 912 loop : -0.56 (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 E 344 PHE 0.013 0.002 PHE D 7 TYR 0.011 0.002 TYR D 337 ARG 0.002 0.000 ARG A 296 *********************** 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 234 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 174 time to evaluate : 1.982 Fit side-chains REVERT: A 41 ARG cc_start: 0.8346 (mtt90) cc_final: 0.8046 (mpt180) REVERT: A 185 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 212 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: B 212 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: C 36 GLU cc_start: 0.8238 (pp20) cc_final: 0.7987 (pp20) REVERT: C 316 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: D 73 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: D 212 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: D 296 ARG cc_start: 0.7348 (ttp-170) cc_final: 0.6687 (ttt-90) REVERT: E 212 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: F 212 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: F 316 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7447 (mp0) outliers start: 60 outliers final: 33 residues processed: 216 average time/residue: 1.5582 time to fit residues: 366.5385 Evaluate side-chains 206 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 63 ASN 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 C residue 316 GLU Chi-restraints excluded: chain C residue 339 THR 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 D residue 212 GLU 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 190 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 316 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16422 Z= 0.211 Angle : 0.487 5.353 22326 Z= 0.246 Chirality : 0.043 0.130 2520 Planarity : 0.004 0.036 2952 Dihedral : 4.414 25.730 2269 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.43 % Allowed : 13.24 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2076 helix: -0.85 (0.50), residues: 126 sheet: 0.11 (0.17), residues: 912 loop : -0.50 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS E 344 PHE 0.031 0.002 PHE D 214 TYR 0.009 0.001 TYR D 337 ARG 0.002 0.000 ARG D 323 *********************** 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 239 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 181 time to evaluate : 2.150 Fit side-chains REVERT: A 41 ARG cc_start: 0.8332 (mtt90) cc_final: 0.8014 (mpt180) REVERT: A 185 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 316 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: B 36 GLU cc_start: 0.8305 (pp20) cc_final: 0.7984 (pp20) REVERT: B 316 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: C 36 GLU cc_start: 0.8201 (pp20) cc_final: 0.7943 (pp20) REVERT: C 292 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9121 (mm) REVERT: D 212 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: D 296 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.6709 (ttt-90) REVERT: E 212 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: F 316 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7429 (mp0) outliers start: 58 outliers final: 26 residues processed: 221 average time/residue: 1.4710 time to fit residues: 356.7335 Evaluate side-chains 206 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 63 ASN 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 B residue 316 GLU Chi-restraints excluded: chain C residue 63 ASN 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 C residue 292 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain D residue 63 ASN 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 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 190 VAL Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 316 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 0.0060 chunk 90 optimal weight: 6.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 110 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16422 Z= 0.197 Angle : 0.479 5.225 22326 Z= 0.243 Chirality : 0.043 0.133 2520 Planarity : 0.004 0.035 2952 Dihedral : 4.304 23.383 2269 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.90 % Allowed : 14.01 % 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 (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: -0.38 (0.18), residues: 2076 helix: -0.75 (0.50), residues: 126 sheet: 0.14 (0.17), residues: 912 loop : -0.45 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.002 0.001 HIS E 344 PHE 0.009 0.001 PHE D 7 TYR 0.009 0.001 TYR E 192 ARG 0.003 0.000 ARG F 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 234 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 185 time to evaluate : 1.891 Fit side-chains REVERT: A 41 ARG cc_start: 0.8304 (mtt90) cc_final: 0.8020 (mpt180) REVERT: A 185 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 316 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: B 36 GLU cc_start: 0.8290 (pp20) cc_final: 0.7970 (pp20) REVERT: B 316 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: C 36 GLU cc_start: 0.8161 (pp20) cc_final: 0.7895 (pp20) REVERT: C 292 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9116 (mm) REVERT: C 316 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: D 73 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8449 (tp30) REVERT: D 212 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: D 296 ARG cc_start: 0.7176 (ttp-170) cc_final: 0.6672 (ttt-90) REVERT: E 212 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: F 63 ASN cc_start: 0.8906 (p0) cc_final: 0.8634 (p0) REVERT: F 316 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7415 (mp0) outliers start: 49 outliers final: 28 residues processed: 219 average time/residue: 1.4618 time to fit residues: 350.5386 Evaluate side-chains 210 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN 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 313 VAL Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 63 ASN 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 292 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 63 ASN 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 D residue 212 GLU 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 190 VAL Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 316 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN B 78 ASN B 263 ASN C 110 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 16422 Z= 0.551 Angle : 0.656 8.580 22326 Z= 0.332 Chirality : 0.049 0.168 2520 Planarity : 0.005 0.045 2952 Dihedral : 5.107 23.711 2269 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.14 % Allowed : 13.36 % 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: -0.51 (0.18), residues: 2076 helix: -1.00 (0.48), residues: 126 sheet: 0.13 (0.17), residues: 912 loop : -0.59 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 173 HIS 0.004 0.002 HIS E 344 PHE 0.033 0.003 PHE E 214 TYR 0.018 0.002 TYR D 337 ARG 0.006 0.001 ARG F 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 228 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 158 time to evaluate : 1.869 Fit side-chains REVERT: A 185 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7957 (mt-10) REVERT: A 316 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: B 36 GLU cc_start: 0.8316 (pp20) cc_final: 0.8007 (pp20) REVERT: C 292 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9212 (mm) REVERT: C 316 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: D 73 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: D 212 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: D 296 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.6739 (ttt-90) REVERT: E 212 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: F 212 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: F 316 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7432 (mp0) outliers start: 70 outliers final: 34 residues processed: 214 average time/residue: 1.5125 time to fit residues: 353.0666 Evaluate side-chains 196 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN 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 A residue 316 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 46 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 B residue 313 VAL Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 63 ASN 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 292 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 37 SER 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 D residue 212 GLU Chi-restraints excluded: chain D residue 215 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 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 316 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 182 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 A 344 HIS C 78 ASN C 110 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16422 Z= 0.139 Angle : 0.451 5.054 22326 Z= 0.230 Chirality : 0.042 0.130 2520 Planarity : 0.004 0.034 2952 Dihedral : 4.220 22.945 2269 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.95 % Allowed : 15.48 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2076 helix: -0.71 (0.50), residues: 126 sheet: 0.12 (0.17), residues: 906 loop : -0.42 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS C 309 PHE 0.009 0.001 PHE C 89 TYR 0.008 0.001 TYR E 192 ARG 0.002 0.000 ARG D 323 *********************** 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 215 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 1.779 Fit side-chains REVERT: A 41 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8062 (mpt180) REVERT: A 185 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7961 (mt-10) REVERT: B 36 GLU cc_start: 0.8308 (pp20) cc_final: 0.8010 (pp20) REVERT: C 316 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: D 296 ARG cc_start: 0.7101 (ttp-170) cc_final: 0.6720 (ttt-90) REVERT: E 296 ARG cc_start: 0.7420 (ttt180) cc_final: 0.7000 (ttt-90) outliers start: 33 outliers final: 19 residues processed: 207 average time/residue: 1.4894 time to fit residues: 336.9850 Evaluate side-chains 196 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 37 SER 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 239 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 134 optimal weight: 0.0020 chunk 203 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 153 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16422 Z= 0.234 Angle : 0.500 5.707 22326 Z= 0.253 Chirality : 0.043 0.140 2520 Planarity : 0.004 0.035 2952 Dihedral : 4.416 23.369 2269 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.89 % Allowed : 15.66 % 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: -0.31 (0.18), residues: 2076 helix: -0.67 (0.50), residues: 126 sheet: 0.19 (0.17), residues: 912 loop : -0.40 (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 E 344 PHE 0.034 0.002 PHE E 214 TYR 0.010 0.001 TYR E 192 ARG 0.002 0.000 ARG F 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 206 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.767 Fit side-chains REVERT: A 41 ARG cc_start: 0.8356 (mtt90) cc_final: 0.8051 (mpt180) REVERT: A 185 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7972 (mt-10) REVERT: A 316 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: C 316 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: D 296 ARG cc_start: 0.7211 (ttp-170) cc_final: 0.6693 (ttt-90) outliers start: 32 outliers final: 24 residues processed: 201 average time/residue: 1.4771 time to fit residues: 325.3812 Evaluate side-chains 199 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 316 GLU 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 63 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 37 SER 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 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 215 ASP Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 23 optimal weight: 0.0030 chunk 44 optimal weight: 0.0570 chunk 162 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 153 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.083239 restraints weight = 20983.756| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.47 r_work: 0.2822 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16422 Z= 0.273 Angle : 0.521 6.241 22326 Z= 0.263 Chirality : 0.044 0.140 2520 Planarity : 0.004 0.036 2952 Dihedral : 4.546 23.097 2269 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.13 % Allowed : 15.37 % 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: -0.32 (0.18), residues: 2076 helix: -0.69 (0.50), residues: 126 sheet: 0.18 (0.17), residues: 912 loop : -0.41 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS E 344 PHE 0.013 0.002 PHE D 7 TYR 0.010 0.001 TYR E 192 ARG 0.002 0.000 ARG F 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5821.58 seconds wall clock time: 104 minutes 6.39 seconds (6246.39 seconds total)