Starting phenix.real_space_refine on Wed Feb 4 05:54:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1k_70010/02_2026/9o1k_70010_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1k_70010/02_2026/9o1k_70010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1k_70010/02_2026/9o1k_70010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1k_70010/02_2026/9o1k_70010.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1k_70010/02_2026/9o1k_70010_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1k_70010/02_2026/9o1k_70010_neut.cif" } resolution = 3.01 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= 0.000 sd= 0.006 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 65 5.16 5 C 6064 2.51 5 N 1432 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9090 Number of models: 1 Model: "" Number of chains: 13 Chain: "I" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "J" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "M" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "N" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "O" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "P" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 591 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "R" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "X" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Y" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2243 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 275} Time building chain proxies: 2.18, per 1000 atoms: 0.24 Number of scatterers: 9090 At special positions: 0 Unit cell: (87.15, 100.43, 112.88, 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 65 16.00 O 1529 8.00 N 1432 7.00 C 6064 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: 0.66 Conformation dependent library (CDL) restraints added in 326.5 milliseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 1 sheets defined 89.9% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'I' and resid 1 through 41 removed outlier: 3.550A pdb=" N ALA I 9 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE I 10 " --> pdb=" O GLY I 6 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 60 removed outlier: 3.500A pdb=" N GLY I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 76 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 2 through 41 removed outlier: 3.666A pdb=" N ILE J 10 " --> pdb=" O GLY J 6 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.673A pdb=" N LEU J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 3.579A pdb=" N ILE J 65 " --> pdb=" O ALA J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'L' and resid 2 through 41 removed outlier: 3.837A pdb=" N ILE L 10 " --> pdb=" O GLY L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 76 removed outlier: 3.756A pdb=" N VAL L 50 " --> pdb=" O PRO L 46 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU L 58 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE L 65 " --> pdb=" O ALA L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 3.919A pdb=" N GLY L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN L 82 " --> pdb=" O PRO L 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 77 through 82' Processing helix chain 'M' and resid 2 through 41 removed outlier: 3.502A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 76 removed outlier: 3.831A pdb=" N VAL M 50 " --> pdb=" O PRO M 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU M 58 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 83 removed outlier: 3.895A pdb=" N GLY M 81 " --> pdb=" O ASN M 77 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN M 82 " --> pdb=" O PRO M 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 41 removed outlier: 3.926A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN N 41 " --> pdb=" O GLY N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 60 removed outlier: 4.042A pdb=" N LEU N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 75 removed outlier: 3.739A pdb=" N MET N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE N 75 " --> pdb=" O LEU N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 3.999A pdb=" N GLY N 81 " --> pdb=" O ASN N 77 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN N 82 " --> pdb=" O PRO N 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 77 through 82' Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.583A pdb=" N ALA O 9 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE O 10 " --> pdb=" O GLY O 6 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 75 removed outlier: 3.591A pdb=" N VAL O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU O 58 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.781A pdb=" N ILE O 83 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 41 removed outlier: 3.546A pdb=" N ALA P 9 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE P 10 " --> pdb=" O GLY P 6 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY P 19 " --> pdb=" O LEU P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 removed outlier: 3.769A pdb=" N VAL P 50 " --> pdb=" O PRO P 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU P 58 " --> pdb=" O ILE P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 removed outlier: 3.527A pdb=" N ILE P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 41 removed outlier: 3.537A pdb=" N ILE Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.599A pdb=" N VAL Q 50 " --> pdb=" O PRO Q 46 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU Q 58 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 76 removed outlier: 3.635A pdb=" N ILE Q 65 " --> pdb=" O ALA Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.720A pdb=" N ILE Q 83 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 41 removed outlier: 3.520A pdb=" N ALA R 9 " --> pdb=" O VAL R 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE R 10 " --> pdb=" O GLY R 6 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.841A pdb=" N VAL R 50 " --> pdb=" O PRO R 46 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 76 removed outlier: 3.512A pdb=" N ILE R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 41 removed outlier: 3.740A pdb=" N ILE S 10 " --> pdb=" O GLY S 6 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 76 removed outlier: 3.651A pdb=" N VAL S 50 " --> pdb=" O PRO S 46 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR S 63 " --> pdb=" O LEU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'X' and resid 5 through 25 Processing helix chain 'X' and resid 25 through 53 removed outlier: 3.880A pdb=" N VAL X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 58 removed outlier: 3.599A pdb=" N ALA X 57 " --> pdb=" O ASP X 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 25 Processing helix chain 'Y' and resid 25 through 52 removed outlier: 3.757A pdb=" N VAL Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 Processing helix chain 'a' and resid 32 through 39 removed outlier: 3.756A pdb=" N MET a 39 " --> pdb=" O GLN a 35 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 68 removed outlier: 3.682A pdb=" N ALA a 66 " --> pdb=" O ILE a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 97 removed outlier: 3.700A pdb=" N PHE a 81 " --> pdb=" O GLY a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 121 removed outlier: 3.660A pdb=" N ILE a 121 " --> pdb=" O LEU a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 138 Processing helix chain 'a' and resid 151 through 175 removed outlier: 3.693A pdb=" N THR a 155 " --> pdb=" O ASP a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 186 removed outlier: 3.891A pdb=" N HIS a 186 " --> pdb=" O GLU a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 241 removed outlier: 4.046A pdb=" N LEU a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Proline residue: a 201 - end of helix removed outlier: 4.073A pdb=" N VAL a 209 " --> pdb=" O LEU a 205 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS a 214 " --> pdb=" O THR a 210 " (cutoff:3.500A) Proline residue: a 215 - end of helix removed outlier: 4.134A pdb=" N ASN a 225 " --> pdb=" O ARG a 221 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET a 226 " --> pdb=" O LEU a 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET a 239 " --> pdb=" O LEU a 235 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE a 240 " --> pdb=" O ILE a 236 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY a 241 " --> pdb=" O ALA a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 283 removed outlier: 4.240A pdb=" N LEU a 264 " --> pdb=" O VAL a 260 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE a 265 " --> pdb=" O PHE a 261 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR a 267 " --> pdb=" O ILE a 263 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 18 through 19 824 hydrogen bonds defined for protein. 2445 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: 1.44 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1441 1.28 - 1.41: 2231 1.41 - 1.55: 5451 1.55 - 1.68: 10 1.68 - 1.82: 128 Bond restraints: 9261 Sorted by residual: bond pdb=" N GLN R 82 " pdb=" CA GLN R 82 " ideal model delta sigma weight residual 1.456 1.523 -0.068 1.32e-02 5.74e+03 2.62e+01 bond pdb=" C GLN P 82 " pdb=" O GLN P 82 " ideal model delta sigma weight residual 1.238 1.145 0.093 1.83e-02 2.99e+03 2.56e+01 bond pdb=" N HIS a 285 " pdb=" CA HIS a 285 " ideal model delta sigma weight residual 1.454 1.519 -0.065 1.40e-02 5.10e+03 2.18e+01 bond pdb=" C GLN P 82 " pdb=" N ILE P 83 " ideal model delta sigma weight residual 1.329 1.382 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" CZ ARG I 40 " pdb=" NH2 ARG I 40 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.52e+00 ... (remaining 9256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.21: 12544 7.21 - 14.42: 6 14.42 - 21.63: 1 21.63 - 28.84: 0 28.84 - 36.05: 2 Bond angle restraints: 12553 Sorted by residual: angle pdb=" O ALA a 284 " pdb=" C ALA a 284 " pdb=" N HIS a 285 " ideal model delta sigma weight residual 122.34 90.90 31.44 1.25e+00 6.40e-01 6.33e+02 angle pdb=" O GLY R 81 " pdb=" C GLY R 81 " pdb=" N GLN R 82 " ideal model delta sigma weight residual 122.42 86.37 36.05 1.59e+00 3.96e-01 5.14e+02 angle pdb=" O GLN P 82 " pdb=" C GLN P 82 " pdb=" N ILE P 83 " ideal model delta sigma weight residual 122.00 110.12 11.88 1.25e+00 6.40e-01 9.03e+01 angle pdb=" C ALA a 284 " pdb=" N HIS a 285 " pdb=" CA HIS a 285 " ideal model delta sigma weight residual 121.99 136.70 -14.71 1.56e+00 4.11e-01 8.89e+01 angle pdb=" CA GLN P 82 " pdb=" C GLN P 82 " pdb=" N ILE P 83 " ideal model delta sigma weight residual 118.30 108.55 9.75 1.26e+00 6.30e-01 5.99e+01 ... (remaining 12548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4991 17.96 - 35.91: 283 35.91 - 53.87: 44 53.87 - 71.83: 8 71.83 - 89.78: 7 Dihedral angle restraints: 5333 sinusoidal: 1957 harmonic: 3376 Sorted by residual: dihedral pdb=" C ILE L 83 " pdb=" N ILE L 83 " pdb=" CA ILE L 83 " pdb=" CB ILE L 83 " ideal model delta harmonic sigma weight residual -122.00 -134.23 12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" C ASP a 127 " pdb=" N ASP a 127 " pdb=" CA ASP a 127 " pdb=" CB ASP a 127 " ideal model delta harmonic sigma weight residual -122.60 -133.90 11.30 0 2.50e+00 1.60e-01 2.04e+01 dihedral pdb=" C ILE a 200 " pdb=" N ILE a 200 " pdb=" CA ILE a 200 " pdb=" CB ILE a 200 " ideal model delta harmonic sigma weight residual -122.00 -132.84 10.84 0 2.50e+00 1.60e-01 1.88e+01 ... (remaining 5330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 840 0.076 - 0.152: 571 0.152 - 0.228: 106 0.228 - 0.304: 18 0.304 - 0.380: 9 Chirality restraints: 1544 Sorted by residual: chirality pdb=" CA ASP a 127 " pdb=" N ASP a 127 " pdb=" C ASP a 127 " pdb=" CB ASP a 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA PHE M 53 " pdb=" N PHE M 53 " pdb=" C PHE M 53 " pdb=" CB PHE M 53 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASP I 60 " pdb=" N ASP I 60 " pdb=" C ASP I 60 " pdb=" CB ASP I 60 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 1541 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 81 " 0.124 2.00e-02 2.50e+03 1.98e-01 3.92e+02 pdb=" C GLY R 81 " -0.343 2.00e-02 2.50e+03 pdb=" O GLY R 81 " 0.112 2.00e-02 2.50e+03 pdb=" N GLN R 82 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 284 " -0.108 2.00e-02 2.50e+03 1.78e-01 3.17e+02 pdb=" C ALA a 284 " 0.308 2.00e-02 2.50e+03 pdb=" O ALA a 284 " -0.107 2.00e-02 2.50e+03 pdb=" N HIS a 285 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN P 82 " -0.082 2.00e-02 2.50e+03 1.64e-01 2.70e+02 pdb=" C GLN P 82 " 0.283 2.00e-02 2.50e+03 pdb=" O GLN P 82 " -0.118 2.00e-02 2.50e+03 pdb=" N ILE P 83 " -0.083 2.00e-02 2.50e+03 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 3678 2.95 - 3.44: 9748 3.44 - 3.92: 15134 3.92 - 4.41: 16276 4.41 - 4.90: 28636 Nonbonded interactions: 73472 Sorted by model distance: nonbonded pdb=" N GLN P 82 " pdb=" N ILE P 83 " model vdw 2.461 2.560 nonbonded pdb=" OD1 ASN a 24 " pdb=" N GLY a 25 " model vdw 2.515 3.120 nonbonded pdb=" O ILE Y 3 " pdb=" OG1 THR Y 6 " model vdw 2.531 3.040 nonbonded pdb=" O PRO P 78 " pdb=" OE1 GLN P 82 " model vdw 2.548 3.040 nonbonded pdb=" N ALA J 76 " pdb=" O ALA J 76 " model vdw 2.556 2.496 ... (remaining 73467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'I' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'J' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'L' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'M' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'N' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'O' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = chain 'P' selection = (chain 'Q' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'R' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'S' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.840 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.012 0.093 9261 Z= 0.708 Angle : 1.803 36.052 12553 Z= 1.251 Chirality : 0.096 0.380 1544 Planarity : 0.014 0.198 1556 Dihedral : 11.898 89.782 3181 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.33 % Allowed : 5.01 % Favored : 94.67 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -1.35 (0.21), residues: 1206 helix: -0.60 (0.14), residues: 1038 sheet: None (None), residues: 0 loop : -1.70 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 40 TYR 0.077 0.020 TYR a 9 PHE 0.070 0.010 PHE X 14 TRP 0.078 0.019 TRP a 114 HIS 0.012 0.003 HIS a 285 Details of bonding type rmsd covalent geometry : bond 0.01164 ( 9261) covalent geometry : angle 1.80338 (12553) hydrogen bonds : bond 0.21121 ( 824) hydrogen bonds : angle 7.30464 ( 2445) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 274 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: I 64 MET cc_start: 0.7851 (mmm) cc_final: 0.7499 (mmt) REVERT: X 23 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7694 (mmmt) outliers start: 3 outliers final: 2 residues processed: 276 average time/residue: 0.0914 time to fit residues: 34.7031 Evaluate side-chains 209 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 49 GLN I 82 GLN J 82 GLN L 82 GLN N 49 GLN Q 77 ASN R 41 GLN S 41 GLN Y 4 ASN Y 48 ASN a 74 GLN a 153 ASN ** a 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 225 ASN a 255 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.120013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087176 restraints weight = 12690.877| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.01 r_work: 0.3104 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9261 Z= 0.161 Angle : 0.658 7.916 12553 Z= 0.344 Chirality : 0.041 0.201 1544 Planarity : 0.005 0.033 1556 Dihedral : 4.155 42.053 1250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.72 % Allowed : 11.97 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 1.67 (0.23), residues: 1206 helix: 1.46 (0.16), residues: 1042 sheet: None (None), residues: 0 loop : -0.96 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 40 TYR 0.006 0.001 TYR a 9 PHE 0.018 0.001 PHE a 179 TRP 0.017 0.002 TRP X 26 HIS 0.002 0.001 HIS a 45 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9261) covalent geometry : angle 0.65849 (12553) hydrogen bonds : bond 0.05880 ( 824) hydrogen bonds : angle 4.27122 ( 2445) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.272 Fit side-chains REVERT: L 40 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7616 (ttm110) REVERT: L 44 MET cc_start: 0.8431 (mmp) cc_final: 0.8129 (mmm) REVERT: L 64 MET cc_start: 0.8908 (mmt) cc_final: 0.8356 (mmt) REVERT: M 41 GLN cc_start: 0.8160 (mp10) cc_final: 0.7303 (mp10) REVERT: O 40 ARG cc_start: 0.8677 (tpp80) cc_final: 0.8367 (tpp80) REVERT: P 36 GLU cc_start: 0.8602 (tt0) cc_final: 0.8332 (tt0) REVERT: X 1 MET cc_start: 0.6442 (mtp) cc_final: 0.6206 (mtt) REVERT: X 23 LYS cc_start: 0.7522 (mmtt) cc_final: 0.7289 (tppt) REVERT: X 38 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8613 (tmmt) REVERT: X 52 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7915 (mmm160) REVERT: X 55 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7893 (pt0) REVERT: a 59 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7421 (t80) REVERT: a 68 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7774 (ttpt) outliers start: 25 outliers final: 13 residues processed: 245 average time/residue: 0.0837 time to fit residues: 28.1696 Evaluate side-chains 216 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 38 LYS Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 252 VAL Chi-restraints excluded: chain a residue 268 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN L 82 GLN a 186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.118843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086363 restraints weight = 12721.106| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.00 r_work: 0.3096 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9261 Z= 0.150 Angle : 0.587 7.791 12553 Z= 0.301 Chirality : 0.039 0.182 1544 Planarity : 0.004 0.040 1556 Dihedral : 3.916 39.899 1249 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.48 % Allowed : 13.93 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 2.40 (0.24), residues: 1206 helix: 1.96 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -0.83 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 40 TYR 0.008 0.001 TYR a 9 PHE 0.014 0.001 PHE N 75 TRP 0.019 0.001 TRP X 26 HIS 0.002 0.001 HIS a 45 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9261) covalent geometry : angle 0.58655 (12553) hydrogen bonds : bond 0.05113 ( 824) hydrogen bonds : angle 3.92817 ( 2445) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.303 Fit side-chains REVERT: L 36 GLU cc_start: 0.8696 (tt0) cc_final: 0.8412 (tt0) REVERT: L 40 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7498 (ttm110) REVERT: M 41 GLN cc_start: 0.8040 (mp10) cc_final: 0.7188 (mp10) REVERT: N 41 GLN cc_start: 0.4558 (mm-40) cc_final: 0.3880 (tp40) REVERT: P 33 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8800 (mmtt) REVERT: P 36 GLU cc_start: 0.8551 (tt0) cc_final: 0.8276 (tt0) REVERT: X 52 ARG cc_start: 0.8153 (ptm160) cc_final: 0.7877 (mmm160) REVERT: Y 17 PHE cc_start: 0.8462 (t80) cc_final: 0.8151 (t80) REVERT: a 59 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7308 (t80) outliers start: 32 outliers final: 18 residues processed: 227 average time/residue: 0.0863 time to fit residues: 26.7587 Evaluate side-chains 222 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain a residue 13 HIS Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain a residue 131 MET Chi-restraints excluded: chain a residue 141 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 252 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN L 82 GLN Y 10 GLN a 186 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.119014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.086308 restraints weight = 12840.610| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.02 r_work: 0.3093 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9261 Z= 0.144 Angle : 0.564 7.187 12553 Z= 0.289 Chirality : 0.038 0.170 1544 Planarity : 0.004 0.041 1556 Dihedral : 3.871 39.294 1249 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.37 % Allowed : 14.69 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 2.66 (0.24), residues: 1206 helix: 2.13 (0.16), residues: 1045 sheet: None (None), residues: 0 loop : -0.70 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 40 TYR 0.007 0.001 TYR a 9 PHE 0.012 0.001 PHE X 14 TRP 0.014 0.001 TRP X 26 HIS 0.002 0.000 HIS a 45 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9261) covalent geometry : angle 0.56436 (12553) hydrogen bonds : bond 0.04741 ( 824) hydrogen bonds : angle 3.76434 ( 2445) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: I 44 MET cc_start: 0.8673 (mmm) cc_final: 0.8382 (mmm) REVERT: L 36 GLU cc_start: 0.8704 (tt0) cc_final: 0.8445 (tt0) REVERT: L 40 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7476 (ttm110) REVERT: M 41 GLN cc_start: 0.8011 (mp10) cc_final: 0.6968 (mp10) REVERT: N 41 GLN cc_start: 0.4861 (mm-40) cc_final: 0.3393 (mm-40) REVERT: P 36 GLU cc_start: 0.8597 (tt0) cc_final: 0.8336 (tt0) REVERT: Y 35 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8184 (mm-30) REVERT: a 59 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7749 (t80) REVERT: a 239 MET cc_start: 0.8446 (mtp) cc_final: 0.7016 (mmt) outliers start: 31 outliers final: 18 residues processed: 223 average time/residue: 0.0925 time to fit residues: 28.2581 Evaluate side-chains 222 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 13 HIS Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain a residue 141 HIS Chi-restraints excluded: chain a residue 252 VAL Chi-restraints excluded: chain a residue 267 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN L 82 GLN O 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.119785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.087346 restraints weight = 12761.518| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.02 r_work: 0.3111 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9261 Z= 0.132 Angle : 0.552 7.332 12553 Z= 0.281 Chirality : 0.037 0.173 1544 Planarity : 0.004 0.042 1556 Dihedral : 3.793 38.155 1249 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.61 % Allowed : 15.67 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 2.87 (0.24), residues: 1206 helix: 2.28 (0.16), residues: 1046 sheet: None (None), residues: 0 loop : -0.71 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 40 TYR 0.007 0.001 TYR a 9 PHE 0.012 0.001 PHE X 14 TRP 0.013 0.001 TRP X 26 HIS 0.001 0.000 HIS a 45 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9261) covalent geometry : angle 0.55172 (12553) hydrogen bonds : bond 0.04411 ( 824) hydrogen bonds : angle 3.66310 ( 2445) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.279 Fit side-chains REVERT: I 44 MET cc_start: 0.8645 (mmm) cc_final: 0.8309 (mmm) REVERT: L 40 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7510 (ttm110) REVERT: M 40 ARG cc_start: 0.8627 (ttm110) cc_final: 0.8232 (ttm-80) REVERT: M 41 GLN cc_start: 0.7932 (mp10) cc_final: 0.7074 (mp10) REVERT: N 41 GLN cc_start: 0.4998 (mm-40) cc_final: 0.3565 (mm-40) REVERT: O 52 MET cc_start: 0.8978 (ttp) cc_final: 0.8701 (ttp) REVERT: P 36 GLU cc_start: 0.8609 (tt0) cc_final: 0.8374 (tt0) REVERT: Y 39 LYS cc_start: 0.7109 (mmtp) cc_final: 0.6824 (tttm) REVERT: a 59 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7666 (t80) REVERT: a 239 MET cc_start: 0.8393 (mtp) cc_final: 0.6938 (mmt) outliers start: 24 outliers final: 16 residues processed: 231 average time/residue: 0.0926 time to fit residues: 29.0537 Evaluate side-chains 222 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 13 HIS Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain a residue 141 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 252 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN L 82 GLN Y 10 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.085109 restraints weight = 13163.805| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.15 r_work: 0.2971 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9261 Z= 0.192 Angle : 0.615 9.080 12553 Z= 0.311 Chirality : 0.039 0.173 1544 Planarity : 0.004 0.043 1556 Dihedral : 3.719 29.323 1246 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.16 % Allowed : 16.32 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 2.71 (0.23), residues: 1206 helix: 2.15 (0.15), residues: 1042 sheet: None (None), residues: 0 loop : -0.54 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 40 TYR 0.010 0.001 TYR a 9 PHE 0.013 0.001 PHE X 14 TRP 0.011 0.001 TRP X 26 HIS 0.002 0.001 HIS a 45 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9261) covalent geometry : angle 0.61544 (12553) hydrogen bonds : bond 0.05104 ( 824) hydrogen bonds : angle 3.76313 ( 2445) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 44 MET cc_start: 0.8738 (mmm) cc_final: 0.8361 (mmm) REVERT: L 36 GLU cc_start: 0.8647 (tt0) cc_final: 0.8372 (tt0) REVERT: L 40 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7655 (ttm110) REVERT: M 41 GLN cc_start: 0.8060 (mp10) cc_final: 0.7150 (mp10) REVERT: N 41 GLN cc_start: 0.5112 (mm-40) cc_final: 0.4150 (mm-40) REVERT: P 33 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8720 (mmtt) REVERT: P 36 GLU cc_start: 0.8636 (tt0) cc_final: 0.8351 (tt0) REVERT: Y 39 LYS cc_start: 0.7245 (mmtp) cc_final: 0.6883 (tttm) outliers start: 29 outliers final: 21 residues processed: 219 average time/residue: 0.0861 time to fit residues: 25.7700 Evaluate side-chains 222 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 13 HIS Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain a residue 131 MET Chi-restraints excluded: chain a residue 141 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 252 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 62 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN L 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.087113 restraints weight = 12929.987| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.06 r_work: 0.3171 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9261 Z= 0.130 Angle : 0.559 8.914 12553 Z= 0.285 Chirality : 0.037 0.181 1544 Planarity : 0.004 0.042 1556 Dihedral : 3.627 27.796 1246 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.85 % Allowed : 17.52 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 3.00 (0.24), residues: 1206 helix: 2.36 (0.16), residues: 1043 sheet: None (None), residues: 0 loop : -0.57 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 40 TYR 0.006 0.001 TYR a 9 PHE 0.014 0.001 PHE a 59 TRP 0.015 0.001 TRP X 26 HIS 0.001 0.000 HIS a 13 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9261) covalent geometry : angle 0.55859 (12553) hydrogen bonds : bond 0.04313 ( 824) hydrogen bonds : angle 3.63746 ( 2445) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: I 44 MET cc_start: 0.8687 (mmm) cc_final: 0.8335 (mmm) REVERT: L 36 GLU cc_start: 0.8679 (tt0) cc_final: 0.8428 (tt0) REVERT: L 40 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7753 (ttm110) REVERT: M 40 ARG cc_start: 0.8665 (ttm110) cc_final: 0.8252 (ttm-80) REVERT: M 41 GLN cc_start: 0.7992 (mp10) cc_final: 0.7114 (mp10) REVERT: N 41 GLN cc_start: 0.5085 (mm-40) cc_final: 0.3619 (mm-40) REVERT: P 33 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8759 (mmtt) REVERT: P 36 GLU cc_start: 0.8700 (tt0) cc_final: 0.8379 (tt0) REVERT: Y 22 MET cc_start: 0.7912 (ppp) cc_final: 0.7664 (mtt) REVERT: Y 39 LYS cc_start: 0.7305 (mmtp) cc_final: 0.6923 (tttm) REVERT: Y 58 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.5986 (p-80) REVERT: a 239 MET cc_start: 0.8358 (mtp) cc_final: 0.6851 (mmt) outliers start: 17 outliers final: 11 residues processed: 219 average time/residue: 0.0863 time to fit residues: 25.9010 Evaluate side-chains 219 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain a residue 13 HIS Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain a residue 141 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 252 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN L 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.086926 restraints weight = 13003.195| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.06 r_work: 0.3136 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9261 Z= 0.137 Angle : 0.571 8.445 12553 Z= 0.289 Chirality : 0.037 0.177 1544 Planarity : 0.004 0.048 1556 Dihedral : 3.599 27.579 1246 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.29 % Allowed : 17.41 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 3.09 (0.23), residues: 1206 helix: 2.41 (0.15), residues: 1042 sheet: None (None), residues: 0 loop : -0.45 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 40 TYR 0.007 0.001 TYR a 9 PHE 0.014 0.001 PHE a 59 TRP 0.014 0.001 TRP X 26 HIS 0.001 0.000 HIS a 13 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9261) covalent geometry : angle 0.57086 (12553) hydrogen bonds : bond 0.04369 ( 824) hydrogen bonds : angle 3.62374 ( 2445) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 44 MET cc_start: 0.8720 (mmm) cc_final: 0.8353 (mmm) REVERT: J 83 ILE cc_start: 0.8335 (pt) cc_final: 0.8047 (pt) REVERT: L 36 GLU cc_start: 0.8700 (tt0) cc_final: 0.8463 (tt0) REVERT: L 40 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7740 (ttm110) REVERT: M 40 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8220 (ttm-80) REVERT: M 41 GLN cc_start: 0.7976 (mp10) cc_final: 0.7114 (mp10) REVERT: N 41 GLN cc_start: 0.5116 (mm-40) cc_final: 0.4165 (mm-40) REVERT: N 43 GLU cc_start: 0.7578 (pm20) cc_final: 0.7211 (pm20) REVERT: O 36 GLU cc_start: 0.8115 (tt0) cc_final: 0.7746 (mt-10) REVERT: P 36 GLU cc_start: 0.8741 (tt0) cc_final: 0.8377 (tt0) REVERT: S 40 ARG cc_start: 0.8339 (ttm110) cc_final: 0.7910 (mtm110) REVERT: Y 22 MET cc_start: 0.7895 (ppp) cc_final: 0.7653 (mtt) REVERT: Y 39 LYS cc_start: 0.7277 (mmtp) cc_final: 0.6902 (tttm) REVERT: Y 58 HIS cc_start: 0.6273 (OUTLIER) cc_final: 0.5998 (p-80) REVERT: a 239 MET cc_start: 0.8321 (mtp) cc_final: 0.6818 (mmt) outliers start: 21 outliers final: 17 residues processed: 229 average time/residue: 0.0841 time to fit residues: 26.4689 Evaluate side-chains 232 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain a residue 13 HIS Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain a residue 141 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 230 GLU Chi-restraints excluded: chain a residue 252 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN L 82 GLN M 82 GLN Y 10 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.121049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.087573 restraints weight = 12799.242| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.04 r_work: 0.3132 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9261 Z= 0.135 Angle : 0.574 8.190 12553 Z= 0.293 Chirality : 0.037 0.184 1544 Planarity : 0.004 0.048 1556 Dihedral : 3.574 27.245 1246 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.72 % Allowed : 17.08 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 3.12 (0.23), residues: 1206 helix: 2.43 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -0.40 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 40 TYR 0.007 0.001 TYR a 9 PHE 0.014 0.001 PHE a 59 TRP 0.014 0.001 TRP X 26 HIS 0.001 0.000 HIS a 13 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9261) covalent geometry : angle 0.57410 (12553) hydrogen bonds : bond 0.04280 ( 824) hydrogen bonds : angle 3.61611 ( 2445) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 44 MET cc_start: 0.8742 (mmm) cc_final: 0.8363 (mmm) REVERT: J 83 ILE cc_start: 0.8320 (pt) cc_final: 0.8031 (pt) REVERT: L 40 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7732 (ttm110) REVERT: M 33 LYS cc_start: 0.8792 (tptt) cc_final: 0.8415 (tppt) REVERT: M 40 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8195 (ttm-80) REVERT: M 41 GLN cc_start: 0.7902 (mp10) cc_final: 0.7069 (mp10) REVERT: N 41 GLN cc_start: 0.5134 (mm-40) cc_final: 0.4211 (mm-40) REVERT: N 43 GLU cc_start: 0.7505 (pm20) cc_final: 0.7209 (pm20) REVERT: O 36 GLU cc_start: 0.8105 (tt0) cc_final: 0.7847 (mt-10) REVERT: P 36 GLU cc_start: 0.8739 (tt0) cc_final: 0.8497 (tt0) REVERT: S 40 ARG cc_start: 0.8348 (ttm110) cc_final: 0.7920 (mtm110) REVERT: Y 22 MET cc_start: 0.7927 (ppp) cc_final: 0.7682 (mtt) REVERT: Y 39 LYS cc_start: 0.7222 (mmtp) cc_final: 0.6906 (tttm) REVERT: Y 58 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.6063 (p-80) REVERT: a 239 MET cc_start: 0.8294 (mtp) cc_final: 0.6796 (mmt) outliers start: 25 outliers final: 22 residues processed: 228 average time/residue: 0.0851 time to fit residues: 26.4012 Evaluate side-chains 236 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 58 HIS Chi-restraints excluded: chain a residue 13 HIS Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain a residue 131 MET Chi-restraints excluded: chain a residue 141 HIS Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 252 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 0.0270 chunk 18 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 82 GLN Y 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088866 restraints weight = 12907.193| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.06 r_work: 0.3159 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9261 Z= 0.128 Angle : 0.566 8.258 12553 Z= 0.288 Chirality : 0.037 0.188 1544 Planarity : 0.004 0.045 1556 Dihedral : 3.537 26.735 1246 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.50 % Allowed : 16.97 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 3.26 (0.23), residues: 1206 helix: 2.52 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -0.31 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 40 TYR 0.006 0.001 TYR a 9 PHE 0.012 0.001 PHE a 59 TRP 0.016 0.001 TRP X 26 HIS 0.001 0.000 HIS a 13 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9261) covalent geometry : angle 0.56629 (12553) hydrogen bonds : bond 0.04103 ( 824) hydrogen bonds : angle 3.58208 ( 2445) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 44 MET cc_start: 0.8731 (mmm) cc_final: 0.8351 (mmm) REVERT: L 40 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7726 (ttm110) REVERT: L 44 MET cc_start: 0.8410 (tpp) cc_final: 0.7946 (mpp) REVERT: M 33 LYS cc_start: 0.8747 (tptt) cc_final: 0.8519 (tppt) REVERT: M 40 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8157 (ttm-80) REVERT: M 41 GLN cc_start: 0.7783 (mp10) cc_final: 0.6985 (mp10) REVERT: N 41 GLN cc_start: 0.5057 (mm-40) cc_final: 0.3598 (mm-40) REVERT: P 36 GLU cc_start: 0.8712 (tt0) cc_final: 0.8463 (tt0) REVERT: S 40 ARG cc_start: 0.8334 (ttm110) cc_final: 0.7893 (mtm110) REVERT: Y 22 MET cc_start: 0.7927 (ppp) cc_final: 0.7697 (mtt) REVERT: Y 39 LYS cc_start: 0.7341 (mmtp) cc_final: 0.7013 (tttm) REVERT: a 239 MET cc_start: 0.8278 (mtp) cc_final: 0.6770 (mmt) outliers start: 23 outliers final: 19 residues processed: 231 average time/residue: 0.0896 time to fit residues: 28.1016 Evaluate side-chains 234 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 13 HIS Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain a residue 131 MET Chi-restraints excluded: chain a residue 141 HIS Chi-restraints excluded: chain a residue 252 VAL Chi-restraints excluded: chain a residue 263 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 82 GLN Y 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.121612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.088286 restraints weight = 12744.998| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.05 r_work: 0.3144 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9261 Z= 0.137 Angle : 0.587 9.138 12553 Z= 0.297 Chirality : 0.037 0.185 1544 Planarity : 0.004 0.043 1556 Dihedral : 3.534 27.318 1246 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.07 % Allowed : 17.08 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: 3.23 (0.23), residues: 1206 helix: 2.51 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -0.37 (0.43), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 40 TYR 0.007 0.001 TYR a 9 PHE 0.014 0.001 PHE a 59 TRP 0.013 0.001 TRP X 26 HIS 0.001 0.000 HIS a 45 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9261) covalent geometry : angle 0.58687 (12553) hydrogen bonds : bond 0.04198 ( 824) hydrogen bonds : angle 3.58154 ( 2445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2220.54 seconds wall clock time: 38 minutes 35.62 seconds (2315.62 seconds total)