Starting phenix.real_space_refine on Fri Feb 14 04:28:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ucu_20728/02_2025/6ucu_20728_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ucu_20728/02_2025/6ucu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ucu_20728/02_2025/6ucu_20728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ucu_20728/02_2025/6ucu_20728.map" model { file = "/net/cci-nas-00/data/ceres_data/6ucu_20728/02_2025/6ucu_20728_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ucu_20728/02_2025/6ucu_20728_trim.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 2, 'ASP:plan': 1} 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: {'GLN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 2, 'ASP:plan': 1} 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: 5.28, per 1000 atoms: 0.64 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: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.83 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: 2.28 Time building geometry restraints manager: 2.50 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' 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 )))) 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: 1.210 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.850 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- 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= 0.746 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (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 TRP 0.032 0.003 TRP K 42 HIS 0.016 0.004 HIS M 29 PHE 0.017 0.002 PHE I 104 TYR 0.116 0.005 TYR I 114 ARG 0.009 0.002 ARG A 315 *********************** 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 : 0.855 Fit side-chains REVERT: A 239 LYS cc_start: 0.7859 (ttmp) cc_final: 0.7521 (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: 0.2523 time to fit residues: 29.0583 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 : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 E 29 HIS I 95 ASN I 99 GLN I 248 GLN M 29 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123477 restraints weight = 8093.995| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.13 r_work: 0.3499 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8302 Z= 0.195 Angle : 0.681 7.958 10978 Z= 0.339 Chirality : 0.045 0.200 1194 Planarity : 0.005 0.050 1314 Dihedral : 14.730 77.698 1638 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.50 % Allowed : 6.73 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 934 helix: 2.27 (0.26), residues: 346 sheet: -0.38 (0.25), residues: 402 loop : -2.29 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 100 HIS 0.004 0.001 HIS C 43 PHE 0.014 0.001 PHE I 359 TYR 0.010 0.001 TYR A 314 ARG 0.003 0.000 ARG I 261 *********************** 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 54 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.810 Fit side-chains REVERT: A 123 ASP cc_start: 0.7915 (p0) cc_final: 0.7453 (p0) REVERT: A 308 GLU cc_start: 0.7768 (pt0) cc_final: 0.7459 (pt0) REVERT: A 331 LYS cc_start: 0.7982 (tttt) cc_final: 0.6698 (mptt) REVERT: I 123 ASP cc_start: 0.7912 (p0) cc_final: 0.7445 (p0) REVERT: I 308 GLU cc_start: 0.7769 (pt0) cc_final: 0.7463 (pt0) REVERT: I 331 LYS cc_start: 0.7988 (tttt) cc_final: 0.6705 (mptt) outliers start: 4 outliers final: 4 residues processed: 52 average time/residue: 0.2678 time to fit residues: 18.9986 Evaluate side-chains 44 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 87 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.122198 restraints weight = 7784.154| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.79 r_work: 0.3389 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.1857 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= 0.193 Angle : 0.612 7.569 10978 Z= 0.307 Chirality : 0.044 0.228 1194 Planarity : 0.004 0.044 1314 Dihedral : 13.297 71.962 1638 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.00 % Allowed : 7.61 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 934 helix: 2.72 (0.27), residues: 346 sheet: -0.29 (0.25), residues: 406 loop : -1.86 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 PHE 0.014 0.001 PHE A 359 TYR 0.017 0.001 TYR A 79 ARG 0.003 0.000 ARG A 261 *********************** 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 54 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.795 Fit side-chains REVERT: A 79 TYR cc_start: 0.8448 (m-80) cc_final: 0.8148 (m-80) REVERT: A 175 ASP cc_start: 0.8139 (p0) cc_final: 0.7546 (p0) REVERT: A 308 GLU cc_start: 0.7723 (pt0) cc_final: 0.7380 (pt0) REVERT: A 331 LYS cc_start: 0.7921 (tttt) cc_final: 0.6589 (mptt) REVERT: I 79 TYR cc_start: 0.8449 (m-80) cc_final: 0.8148 (m-80) REVERT: I 175 ASP cc_start: 0.8166 (p0) cc_final: 0.7574 (p0) REVERT: I 308 GLU cc_start: 0.7710 (pt0) cc_final: 0.7368 (pt0) REVERT: I 331 LYS cc_start: 0.7914 (tttt) cc_final: 0.6587 (mptt) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.2017 time to fit residues: 15.3314 Evaluate side-chains 48 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 248 GLN Chi-restraints excluded: chain I residue 368 LEU 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 38 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.167109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.124426 restraints weight = 7660.175| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.74 r_work: 0.3376 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8302 Z= 0.194 Angle : 0.600 8.572 10978 Z= 0.298 Chirality : 0.044 0.237 1194 Planarity : 0.004 0.040 1314 Dihedral : 12.654 66.915 1638 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.87 % Allowed : 7.36 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 934 helix: 2.93 (0.27), residues: 346 sheet: -0.31 (0.26), residues: 408 loop : -1.42 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 PHE 0.013 0.001 PHE A 359 TYR 0.013 0.001 TYR I 79 ARG 0.003 0.000 ARG I 261 *********************** 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 62 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.927 Fit side-chains REVERT: A 145 TRP cc_start: 0.8963 (m100) cc_final: 0.8721 (m100) REVERT: A 175 ASP cc_start: 0.8210 (p0) cc_final: 0.7512 (p0) REVERT: A 308 GLU cc_start: 0.7715 (pt0) cc_final: 0.7369 (pt0) REVERT: A 331 LYS cc_start: 0.7883 (tttt) cc_final: 0.6619 (mptt) REVERT: I 145 TRP cc_start: 0.8962 (m100) cc_final: 0.8722 (m100) REVERT: I 175 ASP cc_start: 0.8249 (p0) cc_final: 0.7565 (p0) REVERT: I 308 GLU cc_start: 0.7712 (pt0) cc_final: 0.7368 (pt0) REVERT: I 331 LYS cc_start: 0.7882 (tttt) cc_final: 0.6621 (mptt) outliers start: 15 outliers final: 8 residues processed: 54 average time/residue: 0.1981 time to fit residues: 16.0237 Evaluate side-chains 53 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.169565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123584 restraints weight = 7722.788| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.88 r_work: 0.3353 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.2311 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= 0.205 Angle : 0.591 8.022 10978 Z= 0.294 Chirality : 0.044 0.266 1194 Planarity : 0.004 0.038 1314 Dihedral : 12.297 61.817 1638 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.37 % Allowed : 9.85 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.29), residues: 934 helix: 3.03 (0.27), residues: 346 sheet: -0.33 (0.25), residues: 410 loop : -1.14 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 36 HIS 0.004 0.001 HIS C 43 PHE 0.013 0.001 PHE A 359 TYR 0.014 0.001 TYR A 79 ARG 0.003 0.000 ARG I 261 *********************** 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 67 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.785 Fit side-chains REVERT: A 145 TRP cc_start: 0.8943 (m100) cc_final: 0.8691 (m100) REVERT: A 175 ASP cc_start: 0.8197 (p0) cc_final: 0.7458 (p0) REVERT: A 308 GLU cc_start: 0.7704 (pt0) cc_final: 0.7404 (pt0) REVERT: A 331 LYS cc_start: 0.7801 (tttt) cc_final: 0.6553 (mptt) REVERT: I 145 TRP cc_start: 0.8943 (m100) cc_final: 0.8692 (m100) REVERT: I 175 ASP cc_start: 0.8184 (p0) cc_final: 0.7460 (p0) REVERT: I 308 GLU cc_start: 0.7710 (pt0) cc_final: 0.7412 (pt0) REVERT: I 331 LYS cc_start: 0.7795 (tttt) cc_final: 0.6549 (mptt) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.2216 time to fit residues: 19.0202 Evaluate side-chains 57 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 61 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.165123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119105 restraints weight = 7918.026| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.88 r_work: 0.3298 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8302 Z= 0.322 Angle : 0.659 8.125 10978 Z= 0.329 Chirality : 0.046 0.308 1194 Planarity : 0.005 0.036 1314 Dihedral : 12.567 58.521 1638 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.74 % Allowed : 9.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 934 helix: 3.01 (0.27), residues: 346 sheet: -0.50 (0.25), residues: 408 loop : -1.16 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 36 HIS 0.005 0.001 HIS A 346 PHE 0.011 0.001 PHE I 359 TYR 0.014 0.002 TYR A 232 ARG 0.006 0.001 ARG A 261 *********************** 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 80 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.846 Fit side-chains REVERT: A 175 ASP cc_start: 0.8183 (p0) cc_final: 0.7451 (p0) REVERT: A 298 GLU cc_start: 0.7123 (pp20) cc_final: 0.6866 (pp20) REVERT: A 308 GLU cc_start: 0.7695 (pt0) cc_final: 0.7407 (pt0) REVERT: A 331 LYS cc_start: 0.7845 (tttt) cc_final: 0.6557 (mptt) REVERT: A 360 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5860 (mt-10) REVERT: I 175 ASP cc_start: 0.8241 (p0) cc_final: 0.7539 (p0) REVERT: I 298 GLU cc_start: 0.7118 (pp20) cc_final: 0.6866 (pp20) REVERT: I 308 GLU cc_start: 0.7696 (pt0) cc_final: 0.7409 (pt0) REVERT: I 331 LYS cc_start: 0.7847 (tttt) cc_final: 0.6557 (mptt) REVERT: I 360 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5865 (mt-10) outliers start: 22 outliers final: 10 residues processed: 76 average time/residue: 0.2101 time to fit residues: 22.4204 Evaluate side-chains 66 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.164962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.119204 restraints weight = 7946.819| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.88 r_work: 0.3418 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8302 Z= 0.282 Angle : 0.640 7.728 10978 Z= 0.317 Chirality : 0.045 0.320 1194 Planarity : 0.004 0.036 1314 Dihedral : 12.405 59.615 1638 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.00 % Allowed : 11.85 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 934 helix: 3.27 (0.27), residues: 334 sheet: -0.60 (0.25), residues: 408 loop : -0.64 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.003 0.001 HIS A 346 PHE 0.011 0.001 PHE I 359 TYR 0.016 0.002 TYR A 307 ARG 0.005 0.001 ARG A 261 *********************** 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 74 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.855 Fit side-chains REVERT: A 175 ASP cc_start: 0.8377 (p0) cc_final: 0.7688 (p0) REVERT: A 298 GLU cc_start: 0.7384 (pp20) cc_final: 0.7160 (pp20) REVERT: A 308 GLU cc_start: 0.7978 (pt0) cc_final: 0.7738 (pt0) REVERT: A 331 LYS cc_start: 0.8197 (tttt) cc_final: 0.6922 (mptt) REVERT: I 175 ASP cc_start: 0.8411 (p0) cc_final: 0.7755 (p0) REVERT: I 298 GLU cc_start: 0.7378 (pp20) cc_final: 0.7157 (pp20) REVERT: I 308 GLU cc_start: 0.7975 (pt0) cc_final: 0.7737 (pt0) REVERT: I 331 LYS cc_start: 0.8201 (tttt) cc_final: 0.6926 (mptt) outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.2017 time to fit residues: 19.6887 Evaluate side-chains 72 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 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 206 THR Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 326 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 38 optimal weight: 0.0370 chunk 87 optimal weight: 6.9990 chunk 52 optimal weight: 0.0670 chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.164734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.122233 restraints weight = 7766.085| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.72 r_work: 0.3472 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2866 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= 0.160 Angle : 0.582 7.834 10978 Z= 0.287 Chirality : 0.043 0.304 1194 Planarity : 0.004 0.037 1314 Dihedral : 11.570 58.751 1638 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 11.97 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 934 helix: 3.41 (0.27), residues: 334 sheet: -0.45 (0.25), residues: 406 loop : -0.49 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.004 0.001 HIS C 43 PHE 0.011 0.001 PHE I 359 TYR 0.011 0.001 TYR I 307 ARG 0.002 0.000 ARG I 310 *********************** 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 75 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.793 Fit side-chains REVERT: A 145 TRP cc_start: 0.9127 (m100) cc_final: 0.8713 (m100) REVERT: A 175 ASP cc_start: 0.8376 (p0) cc_final: 0.7666 (p0) REVERT: A 298 GLU cc_start: 0.7434 (pp20) cc_final: 0.7208 (pp20) REVERT: A 308 GLU cc_start: 0.8014 (pt0) cc_final: 0.7753 (pt0) REVERT: A 331 LYS cc_start: 0.8197 (tttt) cc_final: 0.6924 (mptt) REVERT: A 360 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6121 (mt-10) REVERT: A 367 LEU cc_start: 0.6433 (mt) cc_final: 0.6226 (mt) REVERT: I 145 TRP cc_start: 0.9120 (m100) cc_final: 0.8706 (m100) REVERT: I 175 ASP cc_start: 0.8412 (p0) cc_final: 0.7722 (p0) REVERT: I 298 GLU cc_start: 0.7424 (pp20) cc_final: 0.7199 (pp20) REVERT: I 308 GLU cc_start: 0.8016 (pt0) cc_final: 0.7749 (pt0) REVERT: I 331 LYS cc_start: 0.8198 (tttt) cc_final: 0.6925 (mptt) REVERT: I 360 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6125 (mt-10) REVERT: I 367 LEU cc_start: 0.6425 (mt) cc_final: 0.6219 (mt) outliers start: 16 outliers final: 10 residues processed: 71 average time/residue: 0.2014 time to fit residues: 20.2928 Evaluate side-chains 67 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 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 33 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.163295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117509 restraints weight = 8142.045| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.89 r_work: 0.3282 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8302 Z= 0.343 Angle : 0.665 7.990 10978 Z= 0.334 Chirality : 0.047 0.328 1194 Planarity : 0.005 0.037 1314 Dihedral : 12.165 59.114 1638 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.00 % Allowed : 11.72 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.29), residues: 934 helix: 3.25 (0.27), residues: 334 sheet: -0.65 (0.25), residues: 408 loop : -0.46 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 36 HIS 0.004 0.001 HIS I 346 PHE 0.012 0.001 PHE I 201 TYR 0.019 0.002 TYR A 307 ARG 0.005 0.000 ARG I 261 *********************** 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 72 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.853 Fit side-chains REVERT: A 298 GLU cc_start: 0.7238 (pp20) cc_final: 0.6964 (pp20) REVERT: A 308 GLU cc_start: 0.7943 (pt0) cc_final: 0.7677 (pt0) REVERT: A 331 LYS cc_start: 0.8067 (tttt) cc_final: 0.6788 (mttt) REVERT: A 360 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6059 (mt-10) REVERT: I 298 GLU cc_start: 0.7232 (pp20) cc_final: 0.6960 (pp20) REVERT: I 308 GLU cc_start: 0.7943 (pt0) cc_final: 0.7679 (pt0) REVERT: I 331 LYS cc_start: 0.8068 (tttt) cc_final: 0.6787 (mttt) REVERT: I 360 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6062 (mt-10) outliers start: 16 outliers final: 14 residues processed: 66 average time/residue: 0.2056 time to fit residues: 19.4865 Evaluate side-chains 71 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118095 restraints weight = 7828.876| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.70 r_work: 0.3439 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8302 Z= 0.226 Angle : 0.616 8.233 10978 Z= 0.308 Chirality : 0.044 0.308 1194 Planarity : 0.004 0.038 1314 Dihedral : 11.842 56.379 1638 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.24 % Allowed : 12.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 934 helix: 3.34 (0.27), residues: 334 sheet: -0.62 (0.25), residues: 408 loop : -0.40 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 PHE 0.011 0.001 PHE I 126 TYR 0.014 0.001 TYR I 307 ARG 0.004 0.000 ARG A 261 ********************** 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 78 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.814 Fit side-chains REVERT: A 175 ASP cc_start: 0.8441 (p0) cc_final: 0.7814 (p0) REVERT: A 298 GLU cc_start: 0.7376 (pp20) cc_final: 0.7136 (pp20) REVERT: A 308 GLU cc_start: 0.8033 (pt0) cc_final: 0.7807 (pt0) REVERT: A 331 LYS cc_start: 0.8219 (tttt) cc_final: 0.6950 (mptt) REVERT: A 360 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6234 (mt-10) REVERT: I 175 ASP cc_start: 0.8473 (p0) cc_final: 0.7854 (p0) REVERT: I 298 GLU cc_start: 0.7383 (pp20) cc_final: 0.7144 (pp20) REVERT: I 308 GLU cc_start: 0.8029 (pt0) cc_final: 0.7802 (pt0) REVERT: I 331 LYS cc_start: 0.8220 (tttt) cc_final: 0.6949 (mptt) REVERT: I 360 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6242 (mt-10) outliers start: 18 outliers final: 14 residues processed: 72 average time/residue: 0.1971 time to fit residues: 20.2718 Evaluate side-chains 74 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 A residue 368 LEU 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 I residue 368 LEU 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 55 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.162723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116909 restraints weight = 8102.122| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.95 r_work: 0.3302 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8302 Z= 0.229 Angle : 0.621 9.102 10978 Z= 0.308 Chirality : 0.044 0.301 1194 Planarity : 0.005 0.037 1314 Dihedral : 11.648 56.348 1638 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.00 % Allowed : 11.97 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 934 helix: 3.32 (0.27), residues: 334 sheet: -0.61 (0.25), residues: 406 loop : -0.37 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 PHE 0.011 0.001 PHE A 126 TYR 0.015 0.001 TYR I 307 ARG 0.003 0.000 ARG I 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3881.97 seconds wall clock time: 69 minutes 56.08 seconds (4196.08 seconds total)