Starting phenix.real_space_refine on Wed Mar 4 01:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ucu_20728/03_2026/6ucu_20728_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ucu_20728/03_2026/6ucu_20728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ucu_20728/03_2026/6ucu_20728_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ucu_20728/03_2026/6ucu_20728_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ucu_20728/03_2026/6ucu_20728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ucu_20728/03_2026/6ucu_20728.map" } resolution = 3.06 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= 0.002 sd= 0.109 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 22 5.16 5 C 5506 2.51 5 N 1246 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8198 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "M" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 227 Unusual residues: {'LMT': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 160 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 40 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 30 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Chain: "I" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 227 Unusual residues: {'LMT': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 160 Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 40 Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 30 Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Time building chain proxies: 1.67, per 1000 atoms: 0.20 Number of scatterers: 8198 At special positions: 0 Unit cell: (116.15, 141.45, 94.3, 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 22 16.00 O 1424 8.00 N 1246 7.00 C 5506 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: 0.64 Conformation dependent library (CDL) restraints added in 200.4 milliseconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 36.7% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 50 through 56 removed outlier: 3.511A pdb=" N LEU A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.768A pdb=" N GLN A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix removed outlier: 3.537A pdb=" N TRP C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.845A pdb=" N THR D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 removed outlier: 4.092A pdb=" N ASP D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 43 removed outlier: 5.820A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.512A pdb=" N LEU E 54 " --> pdb=" O PHE E 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 56 removed outlier: 3.511A pdb=" N LEU I 55 " --> pdb=" O HIS I 51 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 364 through 373 removed outlier: 3.768A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 135 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 49 Proline residue: K 39 - end of helix removed outlier: 3.537A pdb=" N TRP K 49 " --> pdb=" O VAL K 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 51 removed outlier: 3.845A pdb=" N THR L 34 " --> pdb=" O SER L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 57 removed outlier: 4.092A pdb=" N ASP L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 43 removed outlier: 5.820A pdb=" N ILE M 33 " --> pdb=" O HIS M 29 " (cutoff:3.500A) Proline residue: M 34 - end of helix Processing helix chain 'M' and resid 49 through 55 removed outlier: 3.512A pdb=" N LEU M 54 " --> pdb=" O PHE M 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 93 removed outlier: 6.840A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N CYS A 165 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 194 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 263 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY A 83 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU A 357 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG A 85 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N PHE A 359 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP A 87 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR A 361 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 89 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 93 removed outlier: 6.840A pdb=" N PHE I 98 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N CYS I 165 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR I 194 " --> pdb=" O PRO I 185 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL I 263 " --> pdb=" O VAL I 267 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL I 267 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY I 83 " --> pdb=" O CYS I 355 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU I 357 " --> pdb=" O GLY I 83 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG I 85 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N PHE I 359 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP I 87 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR I 361 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN I 89 " --> pdb=" O THR I 361 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1524 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: 0.96 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1786 1.33 - 1.45: 1768 1.45 - 1.58: 4710 1.58 - 1.70: 2 1.70 - 1.82: 36 Bond restraints: 8302 Sorted by residual: bond pdb=" C7 LMT A 414 " pdb=" C8 LMT A 414 " ideal model delta sigma weight residual 1.529 1.479 0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C7 LMT I 401 " pdb=" C8 LMT I 401 " ideal model delta sigma weight residual 1.529 1.479 0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C ALA L 47 " pdb=" O ALA L 47 " ideal model delta sigma weight residual 1.236 1.206 0.030 1.26e-02 6.30e+03 5.61e+00 bond pdb=" C ALA D 47 " pdb=" O ALA D 47 " ideal model delta sigma weight residual 1.236 1.207 0.030 1.26e-02 6.30e+03 5.52e+00 bond pdb=" C7 LMT A 416 " pdb=" C8 LMT A 416 " ideal model delta sigma weight residual 1.529 1.483 0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 8297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 10241 2.29 - 4.59: 412 4.59 - 6.88: 149 6.88 - 9.18: 126 9.18 - 11.47: 50 Bond angle restraints: 10978 Sorted by residual: angle pdb=" N MET A 94 " pdb=" CA MET A 94 " pdb=" C MET A 94 " ideal model delta sigma weight residual 114.56 119.46 -4.90 1.27e+00 6.20e-01 1.49e+01 angle pdb=" N MET I 94 " pdb=" CA MET I 94 " pdb=" C MET I 94 " ideal model delta sigma weight residual 114.56 119.46 -4.90 1.27e+00 6.20e-01 1.49e+01 angle pdb=" CB LEU A 141 " pdb=" CG LEU A 141 " pdb=" CD2 LEU A 141 " ideal model delta sigma weight residual 110.70 122.17 -11.47 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CB LEU I 141 " pdb=" CG LEU I 141 " pdb=" CD2 LEU I 141 " ideal model delta sigma weight residual 110.70 122.17 -11.47 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CA ASP A 134 " pdb=" CB ASP A 134 " pdb=" CG ASP A 134 " ideal model delta sigma weight residual 112.60 116.00 -3.40 1.00e+00 1.00e+00 1.16e+01 ... (remaining 10973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 4757 21.39 - 42.77: 279 42.77 - 64.15: 60 64.15 - 85.54: 6 85.54 - 106.92: 16 Dihedral angle restraints: 5118 sinusoidal: 2352 harmonic: 2766 Sorted by residual: dihedral pdb=" CA ASN I 95 " pdb=" C ASN I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA HIS I 51 " pdb=" C HIS I 51 " pdb=" N ARG I 52 " pdb=" CA ARG I 52 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 5115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 1192 0.334 - 0.668: 0 0.668 - 1.002: 0 1.002 - 1.336: 0 1.336 - 1.671: 2 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CG LEU A 141 " pdb=" CB LEU A 141 " pdb=" CD1 LEU A 141 " pdb=" CD2 LEU A 141 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.98e+01 chirality pdb=" CG LEU I 141 " pdb=" CB LEU I 141 " pdb=" CD1 LEU I 141 " pdb=" CD2 LEU I 141 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.98e+01 chirality pdb=" CA MET A 94 " pdb=" N MET A 94 " pdb=" C MET A 94 " pdb=" CB MET A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1191 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 114 " -0.049 2.00e-02 2.50e+03 4.88e-02 4.77e+01 pdb=" CG TYR I 114 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 TYR I 114 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR I 114 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR I 114 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR I 114 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR I 114 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR I 114 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " 0.049 2.00e-02 2.50e+03 4.88e-02 4.77e+01 pdb=" CG TYR A 114 " -0.116 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 171 " 0.041 2.00e-02 2.50e+03 4.35e-02 3.79e+01 pdb=" CG TYR I 171 " -0.105 2.00e-02 2.50e+03 pdb=" CD1 TYR I 171 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR I 171 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR I 171 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR I 171 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR I 171 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR I 171 " 0.002 2.00e-02 2.50e+03 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 56 2.60 - 3.17: 6387 3.17 - 3.75: 11133 3.75 - 4.32: 15860 4.32 - 4.90: 28131 Nonbonded interactions: 61567 Sorted by model distance: nonbonded pdb=" OD1 ASN A 179 " pdb=" OG SER A 200 " model vdw 2.022 3.040 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.022 3.040 nonbonded pdb=" OG SER I 312 " pdb=" OG SER J 116 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A 312 " pdb=" OG SER B 116 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A 151 " pdb=" OE1 GLN A 169 " model vdw 2.205 3.040 ... (remaining 61562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 49 through 413 or (resid 414 through 417 and (name C1 or n \ ame C10 or name C11 or name C12 or name C2 or name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name C8 or name C9 )))) selection = (chain 'I' and (resid 49 through 373 or (resid 401 through 417 and (name C1 or n \ ame C10 or name C11 or name C12 or name C2 or name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name C8 or name C9 )))) } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.460 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 0.064 8302 Z= 0.560 Angle : 1.545 11.469 10978 Z= 0.653 Chirality : 0.088 1.671 1194 Planarity : 0.007 0.068 1314 Dihedral : 15.160 106.923 3326 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.12 % Allowed : 3.24 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.25), residues: 934 helix: 0.36 (0.24), residues: 340 sheet: -0.72 (0.25), residues: 400 loop : -2.82 (0.35), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 315 TYR 0.116 0.005 TYR I 114 PHE 0.017 0.002 PHE I 104 TRP 0.032 0.003 TRP K 42 HIS 0.016 0.004 HIS M 29 Details of bonding type rmsd covalent geometry : bond 0.01193 ( 8302) covalent geometry : angle 1.54483 (10978) hydrogen bonds : bond 0.09528 ( 524) hydrogen bonds : angle 6.14982 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.275 Fit side-chains REVERT: A 239 LYS cc_start: 0.7859 (ttmp) cc_final: 0.7520 (mttp) REVERT: A 308 GLU cc_start: 0.7434 (pt0) cc_final: 0.7160 (pt0) REVERT: A 367 LEU cc_start: 0.7317 (mt) cc_final: 0.7061 (mt) REVERT: I 239 LYS cc_start: 0.7857 (ttmp) cc_final: 0.7518 (mttp) REVERT: I 308 GLU cc_start: 0.7426 (pt0) cc_final: 0.7148 (pt0) REVERT: I 367 LEU cc_start: 0.7319 (mt) cc_final: 0.7063 (mt) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1030 time to fit residues: 11.8120 Evaluate side-chains 38 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 99 GLN A 248 GLN C 43 HIS E 29 HIS I 95 ASN I 99 GLN I 248 GLN M 29 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.168019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124990 restraints weight = 7714.648| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.73 r_work: 0.3507 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8302 Z= 0.169 Angle : 0.702 8.325 10978 Z= 0.348 Chirality : 0.046 0.200 1194 Planarity : 0.005 0.049 1314 Dihedral : 14.528 76.688 1638 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.75 % Allowed : 7.23 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.27), residues: 934 helix: 2.26 (0.26), residues: 346 sheet: -0.43 (0.25), residues: 402 loop : -2.31 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 261 TYR 0.011 0.002 TYR A 79 PHE 0.015 0.001 PHE A 359 TRP 0.012 0.002 TRP J 100 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8302) covalent geometry : angle 0.70163 (10978) hydrogen bonds : bond 0.03244 ( 524) hydrogen bonds : angle 4.88688 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.267 Fit side-chains REVERT: A 123 ASP cc_start: 0.7953 (p0) cc_final: 0.7519 (p0) REVERT: A 308 GLU cc_start: 0.7836 (pt0) cc_final: 0.7548 (pt0) REVERT: I 123 ASP cc_start: 0.7951 (p0) cc_final: 0.7509 (p0) REVERT: I 308 GLU cc_start: 0.7836 (pt0) cc_final: 0.7550 (pt0) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.0993 time to fit residues: 6.7971 Evaluate side-chains 40 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN E 43 HIS ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN M 43 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.167807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119251 restraints weight = 8122.916| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.12 r_work: 0.3331 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8302 Z= 0.155 Angle : 0.623 7.476 10978 Z= 0.312 Chirality : 0.044 0.240 1194 Planarity : 0.005 0.044 1314 Dihedral : 13.363 70.940 1638 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.25 % Allowed : 7.48 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.28), residues: 934 helix: 2.74 (0.27), residues: 346 sheet: -0.40 (0.25), residues: 410 loop : -1.81 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.019 0.001 TYR I 79 PHE 0.015 0.001 PHE A 359 TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS I 346 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8302) covalent geometry : angle 0.62297 (10978) hydrogen bonds : bond 0.02939 ( 524) hydrogen bonds : angle 4.63070 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.216 Fit side-chains REVERT: A 79 TYR cc_start: 0.8495 (m-80) cc_final: 0.8203 (m-80) REVERT: A 175 ASP cc_start: 0.8199 (p0) cc_final: 0.7625 (p0) REVERT: A 331 LYS cc_start: 0.8115 (tttt) cc_final: 0.6859 (mptt) REVERT: I 79 TYR cc_start: 0.8495 (m-80) cc_final: 0.8203 (m-80) REVERT: I 175 ASP cc_start: 0.8214 (p0) cc_final: 0.7642 (p0) REVERT: I 331 LYS cc_start: 0.8121 (tttt) cc_final: 0.6864 (mptt) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.0881 time to fit residues: 7.6385 Evaluate side-chains 55 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN L 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.167460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118970 restraints weight = 8232.617| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.12 r_work: 0.3325 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8302 Z= 0.138 Angle : 0.610 8.605 10978 Z= 0.303 Chirality : 0.044 0.240 1194 Planarity : 0.004 0.040 1314 Dihedral : 12.828 66.653 1638 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.62 % Allowed : 8.35 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.29), residues: 934 helix: 2.96 (0.27), residues: 346 sheet: -0.38 (0.25), residues: 410 loop : -1.48 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.014 0.001 TYR A 79 PHE 0.011 0.001 PHE A 359 TRP 0.009 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8302) covalent geometry : angle 0.60961 (10978) hydrogen bonds : bond 0.02680 ( 524) hydrogen bonds : angle 4.50095 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.277 Fit side-chains REVERT: A 175 ASP cc_start: 0.8304 (p0) cc_final: 0.7617 (p0) REVERT: A 308 GLU cc_start: 0.7817 (pt0) cc_final: 0.7542 (pt0) REVERT: A 331 LYS cc_start: 0.7975 (tttt) cc_final: 0.6723 (mptt) REVERT: I 175 ASP cc_start: 0.8339 (p0) cc_final: 0.7662 (p0) REVERT: I 308 GLU cc_start: 0.7812 (pt0) cc_final: 0.7540 (pt0) REVERT: I 331 LYS cc_start: 0.7977 (tttt) cc_final: 0.6726 (mptt) outliers start: 13 outliers final: 8 residues processed: 57 average time/residue: 0.0817 time to fit residues: 6.7756 Evaluate side-chains 56 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 85 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.164409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118639 restraints weight = 8014.778| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.87 r_work: 0.3417 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8302 Z= 0.207 Angle : 0.647 8.542 10978 Z= 0.324 Chirality : 0.046 0.284 1194 Planarity : 0.005 0.037 1314 Dihedral : 12.902 61.152 1638 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.62 % Allowed : 10.97 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.29), residues: 934 helix: 2.94 (0.27), residues: 346 sheet: -0.45 (0.25), residues: 408 loop : -1.29 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 261 TYR 0.017 0.002 TYR A 79 PHE 0.011 0.001 PHE I 126 TRP 0.013 0.001 TRP K 36 HIS 0.004 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 8302) covalent geometry : angle 0.64750 (10978) hydrogen bonds : bond 0.02824 ( 524) hydrogen bonds : angle 4.51914 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.184 Fit side-chains REVERT: A 175 ASP cc_start: 0.8403 (p0) cc_final: 0.7772 (p0) REVERT: A 308 GLU cc_start: 0.7911 (pt0) cc_final: 0.7657 (pt0) REVERT: A 331 LYS cc_start: 0.8126 (tttt) cc_final: 0.6825 (mptt) REVERT: A 369 MET cc_start: 0.6136 (mmm) cc_final: 0.5927 (mmp) REVERT: I 175 ASP cc_start: 0.8370 (p0) cc_final: 0.7714 (p0) REVERT: I 308 GLU cc_start: 0.7911 (pt0) cc_final: 0.7659 (pt0) REVERT: I 331 LYS cc_start: 0.8129 (tttt) cc_final: 0.6826 (mptt) REVERT: I 369 MET cc_start: 0.6136 (mmm) cc_final: 0.5926 (mmp) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 0.0942 time to fit residues: 8.6783 Evaluate side-chains 62 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 4 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN D 50 GLN I 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.159788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117338 restraints weight = 7846.243| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.73 r_work: 0.3311 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8302 Z= 0.180 Angle : 0.622 8.025 10978 Z= 0.308 Chirality : 0.045 0.304 1194 Planarity : 0.004 0.039 1314 Dihedral : 12.702 57.918 1638 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.49 % Allowed : 11.60 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.29), residues: 934 helix: 3.22 (0.27), residues: 334 sheet: -0.54 (0.25), residues: 408 loop : -0.68 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.016 0.002 TYR A 79 PHE 0.012 0.001 PHE A 126 TRP 0.013 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8302) covalent geometry : angle 0.62151 (10978) hydrogen bonds : bond 0.02698 ( 524) hydrogen bonds : angle 4.48553 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.268 Fit side-chains REVERT: A 175 ASP cc_start: 0.8249 (p0) cc_final: 0.7527 (p0) REVERT: A 298 GLU cc_start: 0.7284 (pp20) cc_final: 0.7031 (pp20) REVERT: A 308 GLU cc_start: 0.7878 (pt0) cc_final: 0.7583 (pt0) REVERT: A 331 LYS cc_start: 0.7957 (tttt) cc_final: 0.6643 (mptt) REVERT: A 360 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6031 (mt-10) REVERT: A 369 MET cc_start: 0.6100 (mmm) cc_final: 0.5889 (mmp) REVERT: I 175 ASP cc_start: 0.8257 (p0) cc_final: 0.7533 (p0) REVERT: I 298 GLU cc_start: 0.7279 (pp20) cc_final: 0.7029 (pp20) REVERT: I 308 GLU cc_start: 0.7869 (pt0) cc_final: 0.7569 (pt0) REVERT: I 331 LYS cc_start: 0.7960 (tttt) cc_final: 0.6646 (mptt) REVERT: I 360 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6040 (mt-10) REVERT: I 369 MET cc_start: 0.6106 (mmm) cc_final: 0.5893 (mmp) outliers start: 20 outliers final: 12 residues processed: 68 average time/residue: 0.0910 time to fit residues: 8.7729 Evaluate side-chains 68 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 360 GLU Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.162401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.120048 restraints weight = 7825.820| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.71 r_work: 0.3336 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8302 Z= 0.140 Angle : 0.590 7.590 10978 Z= 0.292 Chirality : 0.044 0.310 1194 Planarity : 0.004 0.036 1314 Dihedral : 12.235 58.239 1638 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.74 % Allowed : 11.60 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 934 helix: 3.33 (0.27), residues: 334 sheet: -0.51 (0.25), residues: 406 loop : -0.57 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.013 0.001 TYR I 307 PHE 0.011 0.001 PHE I 126 TRP 0.012 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8302) covalent geometry : angle 0.58973 (10978) hydrogen bonds : bond 0.02497 ( 524) hydrogen bonds : angle 4.37947 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.196 Fit side-chains REVERT: A 175 ASP cc_start: 0.8220 (p0) cc_final: 0.7482 (p0) REVERT: A 298 GLU cc_start: 0.7281 (pp20) cc_final: 0.7025 (pp20) REVERT: A 308 GLU cc_start: 0.7861 (pt0) cc_final: 0.7552 (pt0) REVERT: A 331 LYS cc_start: 0.8019 (tttt) cc_final: 0.6739 (mptt) REVERT: A 348 LYS cc_start: 0.8528 (ptpt) cc_final: 0.8267 (ptpt) REVERT: A 360 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5991 (mt-10) REVERT: I 175 ASP cc_start: 0.8253 (p0) cc_final: 0.7518 (p0) REVERT: I 298 GLU cc_start: 0.7274 (pp20) cc_final: 0.7020 (pp20) REVERT: I 308 GLU cc_start: 0.7859 (pt0) cc_final: 0.7545 (pt0) REVERT: I 331 LYS cc_start: 0.8012 (tttt) cc_final: 0.6733 (mptt) REVERT: I 348 LYS cc_start: 0.8538 (ptpt) cc_final: 0.8278 (ptpt) REVERT: I 360 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6000 (mt-10) outliers start: 22 outliers final: 14 residues processed: 76 average time/residue: 0.0843 time to fit residues: 9.2309 Evaluate side-chains 73 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 360 GLU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 33 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.0040 chunk 90 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.171081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124002 restraints weight = 8026.563| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.92 r_work: 0.3435 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8302 Z= 0.134 Angle : 0.580 7.804 10978 Z= 0.289 Chirality : 0.044 0.312 1194 Planarity : 0.004 0.037 1314 Dihedral : 11.808 59.396 1638 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.00 % Allowed : 12.09 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.29), residues: 934 helix: 3.36 (0.27), residues: 334 sheet: -0.48 (0.25), residues: 406 loop : -0.48 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.014 0.001 TYR A 307 PHE 0.011 0.001 PHE I 126 TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8302) covalent geometry : angle 0.57995 (10978) hydrogen bonds : bond 0.02454 ( 524) hydrogen bonds : angle 4.32437 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.287 Fit side-chains REVERT: A 145 TRP cc_start: 0.9143 (m100) cc_final: 0.8696 (m100) REVERT: A 175 ASP cc_start: 0.8404 (p0) cc_final: 0.7713 (p0) REVERT: A 298 GLU cc_start: 0.7444 (pp20) cc_final: 0.7218 (pp20) REVERT: A 308 GLU cc_start: 0.8026 (pt0) cc_final: 0.7751 (pt0) REVERT: A 331 LYS cc_start: 0.8183 (tttt) cc_final: 0.6850 (mptt) REVERT: A 348 LYS cc_start: 0.8690 (ptpt) cc_final: 0.8117 (ptpp) REVERT: A 360 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6241 (mt-10) REVERT: I 145 TRP cc_start: 0.9139 (m100) cc_final: 0.8693 (m100) REVERT: I 175 ASP cc_start: 0.8415 (p0) cc_final: 0.7717 (p0) REVERT: I 298 GLU cc_start: 0.7432 (pp20) cc_final: 0.7207 (pp20) REVERT: I 308 GLU cc_start: 0.8021 (pt0) cc_final: 0.7740 (pt0) REVERT: I 331 LYS cc_start: 0.8182 (tttt) cc_final: 0.6847 (mptt) REVERT: I 348 LYS cc_start: 0.8695 (ptpt) cc_final: 0.8127 (ptpp) REVERT: I 360 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6245 (mt-10) outliers start: 16 outliers final: 14 residues processed: 62 average time/residue: 0.0885 time to fit residues: 7.7915 Evaluate side-chains 66 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 360 GLU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 33 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.165358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119524 restraints weight = 7949.376| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.94 r_work: 0.3331 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8302 Z= 0.117 Angle : 0.558 7.694 10978 Z= 0.279 Chirality : 0.043 0.296 1194 Planarity : 0.004 0.037 1314 Dihedral : 11.326 59.414 1638 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.75 % Allowed : 12.34 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.29), residues: 934 helix: 3.41 (0.27), residues: 334 sheet: -0.45 (0.25), residues: 406 loop : -0.31 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.012 0.001 TYR A 307 PHE 0.010 0.001 PHE I 126 TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8302) covalent geometry : angle 0.55847 (10978) hydrogen bonds : bond 0.02326 ( 524) hydrogen bonds : angle 4.24244 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.248 Fit side-chains REVERT: A 145 TRP cc_start: 0.9025 (m100) cc_final: 0.8547 (m100) REVERT: A 175 ASP cc_start: 0.8341 (p0) cc_final: 0.7613 (p0) REVERT: A 298 GLU cc_start: 0.7338 (pp20) cc_final: 0.7059 (pp20) REVERT: A 308 GLU cc_start: 0.7960 (pt0) cc_final: 0.7648 (pt0) REVERT: A 331 LYS cc_start: 0.8044 (tttt) cc_final: 0.6771 (mttp) REVERT: A 348 LYS cc_start: 0.8566 (ptpt) cc_final: 0.7955 (ptpp) REVERT: I 145 TRP cc_start: 0.9018 (m100) cc_final: 0.8541 (m100) REVERT: I 298 GLU cc_start: 0.7332 (pp20) cc_final: 0.7056 (pp20) REVERT: I 308 GLU cc_start: 0.7961 (pt0) cc_final: 0.7649 (pt0) REVERT: I 331 LYS cc_start: 0.8042 (tttt) cc_final: 0.6769 (mttp) REVERT: I 348 LYS cc_start: 0.8572 (ptpt) cc_final: 0.7965 (ptpp) outliers start: 14 outliers final: 12 residues processed: 64 average time/residue: 0.0925 time to fit residues: 8.4187 Evaluate side-chains 64 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.0370 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.171321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124380 restraints weight = 8088.671| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.92 r_work: 0.3437 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8302 Z= 0.137 Angle : 0.576 8.075 10978 Z= 0.288 Chirality : 0.043 0.282 1194 Planarity : 0.004 0.037 1314 Dihedral : 11.140 58.223 1638 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.24 % Allowed : 11.97 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.29), residues: 934 helix: 3.39 (0.27), residues: 334 sheet: -0.45 (0.25), residues: 406 loop : -0.22 (0.51), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 261 TYR 0.014 0.001 TYR A 307 PHE 0.011 0.001 PHE I 126 TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8302) covalent geometry : angle 0.57590 (10978) hydrogen bonds : bond 0.02368 ( 524) hydrogen bonds : angle 4.24778 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.288 Fit side-chains REVERT: A 175 ASP cc_start: 0.8469 (p0) cc_final: 0.7831 (p0) REVERT: A 298 GLU cc_start: 0.7432 (pp20) cc_final: 0.7187 (pp20) REVERT: A 308 GLU cc_start: 0.8055 (pt0) cc_final: 0.7774 (pt0) REVERT: A 331 LYS cc_start: 0.8209 (tttt) cc_final: 0.6939 (mttp) REVERT: A 348 LYS cc_start: 0.8633 (ptpt) cc_final: 0.8031 (ptpp) REVERT: A 360 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6280 (mt-10) REVERT: I 298 GLU cc_start: 0.7423 (pp20) cc_final: 0.7180 (pp20) REVERT: I 308 GLU cc_start: 0.8052 (pt0) cc_final: 0.7769 (pt0) REVERT: I 331 LYS cc_start: 0.8208 (tttt) cc_final: 0.6937 (mttp) REVERT: I 348 LYS cc_start: 0.8641 (ptpt) cc_final: 0.8043 (ptpp) REVERT: I 360 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6288 (mt-10) outliers start: 18 outliers final: 12 residues processed: 63 average time/residue: 0.1006 time to fit residues: 8.6281 Evaluate side-chains 65 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 360 GLU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.0270 chunk 46 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.163718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118077 restraints weight = 8011.886| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.94 r_work: 0.3438 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8302 Z= 0.138 Angle : 0.577 8.239 10978 Z= 0.289 Chirality : 0.043 0.262 1194 Planarity : 0.004 0.037 1314 Dihedral : 10.999 56.858 1638 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.75 % Allowed : 12.59 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 934 helix: 3.18 (0.27), residues: 346 sheet: -0.46 (0.25), residues: 406 loop : -0.66 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 261 TYR 0.014 0.001 TYR A 307 PHE 0.011 0.001 PHE I 126 TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8302) covalent geometry : angle 0.57670 (10978) hydrogen bonds : bond 0.02351 ( 524) hydrogen bonds : angle 4.23302 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1810.86 seconds wall clock time: 31 minutes 44.30 seconds (1904.30 seconds total)