Starting phenix.real_space_refine on Sun Jul 27 22:27:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ucu_20728/07_2025/6ucu_20728_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ucu_20728/07_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_20728/07_2025/6ucu_20728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ucu_20728/07_2025/6ucu_20728.map" model { file = "/net/cci-nas-00/data/ceres_data/6ucu_20728/07_2025/6ucu_20728_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ucu_20728/07_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-5711/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: 5.34, per 1000 atoms: 0.65 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: 2.27 Conformation dependent library (CDL) restraints added in 942.4 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: 0.88 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: 2.40 Time building geometry restraints manager: 2.67 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: 0.04 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: 1.840 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.950 Find NCS groups from input model: 0.390 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.09528 ( 524) hydrogen bonds : angle 6.14982 ( 1524) covalent geometry : bond 0.01193 ( 8302) covalent geometry : angle 1.54483 (10978) *********************** 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 : 0.728 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: 0.2378 time to fit residues: 27.2485 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 : 0.746 ------------------------------------------------------------------------------- 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 = 0.172180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123503 restraints weight = 8091.407| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.12 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: 0.6421 moved from start: 0.1469 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= 0.141 Angle : 0.682 7.955 10978 Z= 0.340 Chirality : 0.045 0.197 1194 Planarity : 0.005 0.050 1314 Dihedral : 14.743 77.631 1638 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.61 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 B 100 HIS 0.004 0.001 HIS C 43 PHE 0.014 0.001 PHE I 359 TYR 0.009 0.001 TYR M 38 ARG 0.003 0.000 ARG I 261 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 524) hydrogen bonds : angle 4.88740 ( 1524) covalent geometry : bond 0.00313 ( 8302) covalent geometry : angle 0.68240 (10978) *********************** 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: 0.7918 (p0) cc_final: 0.7456 (p0) REVERT: A 308 GLU cc_start: 0.7770 (pt0) cc_final: 0.7461 (pt0) REVERT: A 331 LYS cc_start: 0.7982 (tttt) cc_final: 0.6698 (mptt) REVERT: I 123 ASP cc_start: 0.7914 (p0) cc_final: 0.7447 (p0) REVERT: I 308 GLU cc_start: 0.7771 (pt0) cc_final: 0.7465 (pt0) REVERT: I 331 LYS cc_start: 0.7988 (tttt) cc_final: 0.6706 (mptt) outliers start: 4 outliers final: 4 residues processed: 52 average time/residue: 0.3096 time to fit residues: 21.9607 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 : 0.822 ------------------------------------------------------------------------------- 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: 7.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 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 = 0.4013 r_free = 0.4013 target = 0.166479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118005 restraints weight = 8207.931| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.13 r_work: 0.3311 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8302 Z= 0.179 Angle : 0.649 7.379 10978 Z= 0.326 Chirality : 0.046 0.254 1194 Planarity : 0.005 0.044 1314 Dihedral : 13.425 70.718 1638 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.25 % Allowed : 7.61 % Favored : 91.15 % 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: 0.65 (0.28), residues: 934 helix: 2.68 (0.27), residues: 346 sheet: -0.44 (0.25), residues: 410 loop : -1.79 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.005 0.001 HIS I 346 PHE 0.015 0.001 PHE A 359 TYR 0.020 0.002 TYR A 79 ARG 0.005 0.001 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 524) hydrogen bonds : angle 4.65374 ( 1524) covalent geometry : bond 0.00414 ( 8302) covalent geometry : angle 0.64852 (10978) *********************** 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 : 0.841 Fit side-chains REVERT: A 79 TYR cc_start: 0.8478 (m-80) cc_final: 0.8220 (m-80) REVERT: A 175 ASP cc_start: 0.8285 (p0) cc_final: 0.7694 (p0) REVERT: A 308 GLU cc_start: 0.7838 (pt0) cc_final: 0.7521 (pt0) REVERT: A 331 LYS cc_start: 0.8143 (tttt) cc_final: 0.6882 (mptt) REVERT: I 79 TYR cc_start: 0.8484 (m-80) cc_final: 0.8226 (m-80) REVERT: I 175 ASP cc_start: 0.8305 (p0) cc_final: 0.7717 (p0) REVERT: I 308 GLU cc_start: 0.7832 (pt0) cc_final: 0.7516 (pt0) REVERT: I 331 LYS cc_start: 0.8143 (tttt) cc_final: 0.6884 (mptt) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.2681 time to fit residues: 23.7682 Evaluate side-chains 54 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 L 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.161079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115099 restraints weight = 8045.003| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.99 r_work: 0.3325 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.2324 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= 0.150 Angle : 0.614 8.729 10978 Z= 0.305 Chirality : 0.044 0.249 1194 Planarity : 0.004 0.039 1314 Dihedral : 12.914 66.319 1638 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.75 % Allowed : 8.48 % Favored : 89.78 % 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: 0.89 (0.29), residues: 934 helix: 2.92 (0.27), residues: 346 sheet: -0.43 (0.25), residues: 410 loop : -1.45 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 PHE 0.011 0.001 PHE A 359 TYR 0.014 0.001 TYR A 79 ARG 0.004 0.000 ARG I 261 Details of bonding type rmsd hydrogen bonds : bond 0.02722 ( 524) hydrogen bonds : angle 4.52379 ( 1524) covalent geometry : bond 0.00348 ( 8302) covalent geometry : angle 0.61380 (10978) *********************** 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 66 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.779 Fit side-chains REVERT: A 175 ASP cc_start: 0.8336 (p0) cc_final: 0.7681 (p0) REVERT: A 308 GLU cc_start: 0.7803 (pt0) cc_final: 0.7538 (pt0) REVERT: A 331 LYS cc_start: 0.7994 (tttt) cc_final: 0.6741 (mptt) REVERT: I 175 ASP cc_start: 0.8369 (p0) cc_final: 0.7686 (p0) REVERT: I 308 GLU cc_start: 0.7796 (pt0) cc_final: 0.7531 (pt0) REVERT: I 331 LYS cc_start: 0.7989 (tttt) cc_final: 0.6738 (mptt) outliers start: 14 outliers final: 8 residues processed: 62 average time/residue: 0.1946 time to fit residues: 17.3204 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 : 0.759 ------------------------------------------------------------------------------- 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: 1.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.164851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119067 restraints weight = 7857.246| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.85 r_work: 0.3418 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2550 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= 0.205 Angle : 0.644 8.492 10978 Z= 0.321 Chirality : 0.046 0.285 1194 Planarity : 0.005 0.037 1314 Dihedral : 12.948 61.463 1638 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.00 % Allowed : 11.22 % Favored : 86.78 % 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: 0.92 (0.29), residues: 934 helix: 2.94 (0.27), residues: 346 sheet: -0.47 (0.25), residues: 408 loop : -1.26 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.004 0.001 HIS A 346 PHE 0.012 0.001 PHE A 126 TYR 0.017 0.002 TYR I 79 ARG 0.005 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 524) hydrogen bonds : angle 4.53160 ( 1524) covalent geometry : bond 0.00480 ( 8302) covalent geometry : angle 0.64440 (10978) *********************** 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 72 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.888 Fit side-chains REVERT: A 175 ASP cc_start: 0.8402 (p0) cc_final: 0.7771 (p0) REVERT: A 308 GLU cc_start: 0.7911 (pt0) cc_final: 0.7659 (pt0) REVERT: A 331 LYS cc_start: 0.8126 (tttt) cc_final: 0.6826 (mptt) REVERT: A 369 MET cc_start: 0.6245 (mmm) cc_final: 0.6030 (mmp) REVERT: I 175 ASP cc_start: 0.8396 (p0) cc_final: 0.7769 (p0) REVERT: I 308 GLU cc_start: 0.7905 (pt0) cc_final: 0.7655 (pt0) REVERT: I 331 LYS cc_start: 0.8126 (tttt) cc_final: 0.6828 (mptt) REVERT: I 369 MET cc_start: 0.6251 (mmm) cc_final: 0.6035 (mmp) outliers start: 16 outliers final: 12 residues processed: 66 average time/residue: 0.2293 time to fit residues: 20.9527 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 : 0.829 ------------------------------------------------------------------------------- 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 368 LEU Chi-restraints excluded: chain B residue 126 MET 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 368 LEU Chi-restraints excluded: chain J residue 126 MET 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: 0.6980 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 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 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 = 0.162475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120217 restraints weight = 7744.094| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.69 r_work: 0.3330 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.2713 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= 0.152 Angle : 0.604 7.847 10978 Z= 0.299 Chirality : 0.044 0.298 1194 Planarity : 0.004 0.038 1314 Dihedral : 12.545 58.310 1638 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 (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: 1.00 (0.29), residues: 934 helix: 3.04 (0.27), residues: 346 sheet: -0.50 (0.25), residues: 408 loop : -1.10 (0.47), residues: 180 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 A 126 TYR 0.015 0.002 TYR I 79 ARG 0.002 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.02589 ( 524) hydrogen bonds : angle 4.44713 ( 1524) covalent geometry : bond 0.00351 ( 8302) covalent geometry : angle 0.60408 (10978) *********************** 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 75 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.771 Fit side-chains REVERT: A 175 ASP cc_start: 0.8221 (p0) cc_final: 0.7490 (p0) REVERT: A 298 GLU cc_start: 0.7264 (pp20) cc_final: 0.7013 (pp20) REVERT: A 308 GLU cc_start: 0.7819 (pt0) cc_final: 0.7511 (pt0) REVERT: A 331 LYS cc_start: 0.7898 (tttt) cc_final: 0.6592 (mptt) REVERT: A 360 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.5954 (mt-10) REVERT: A 369 MET cc_start: 0.6113 (mmm) cc_final: 0.5881 (mmp) REVERT: I 175 ASP cc_start: 0.8258 (p0) cc_final: 0.7536 (p0) REVERT: I 298 GLU cc_start: 0.7256 (pp20) cc_final: 0.7006 (pp20) REVERT: I 308 GLU cc_start: 0.7813 (pt0) cc_final: 0.7505 (pt0) REVERT: I 331 LYS cc_start: 0.7897 (tttt) cc_final: 0.6591 (mptt) REVERT: I 360 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.5963 (mt-10) REVERT: I 369 MET cc_start: 0.6114 (mmm) cc_final: 0.5881 (mmp) outliers start: 20 outliers final: 10 residues processed: 67 average time/residue: 0.1766 time to fit residues: 17.7591 Evaluate side-chains 65 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 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 63 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.164202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118333 restraints weight = 7970.628| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.94 r_work: 0.3315 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2821 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= 0.139 Angle : 0.588 7.587 10978 Z= 0.292 Chirality : 0.044 0.309 1194 Planarity : 0.004 0.036 1314 Dihedral : 12.108 57.676 1638 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.49 % Allowed : 11.85 % 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: 1.25 (0.29), residues: 934 helix: 3.34 (0.27), residues: 334 sheet: -0.52 (0.25), residues: 408 loop : -0.45 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 PHE 0.011 0.001 PHE A 126 TYR 0.013 0.001 TYR I 307 ARG 0.002 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.02475 ( 524) hydrogen bonds : angle 4.36379 ( 1524) covalent geometry : bond 0.00321 ( 8302) covalent geometry : angle 0.58840 (10978) *********************** 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 79 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.793 Fit side-chains REVERT: A 89 ASN cc_start: 0.7228 (p0) cc_final: 0.6934 (p0) REVERT: A 145 TRP cc_start: 0.9062 (m100) cc_final: 0.8599 (m100) REVERT: A 175 ASP cc_start: 0.8324 (p0) cc_final: 0.7604 (p0) REVERT: A 298 GLU cc_start: 0.7332 (pp20) cc_final: 0.7086 (pp20) REVERT: A 308 GLU cc_start: 0.7939 (pt0) cc_final: 0.7641 (pt0) REVERT: A 331 LYS cc_start: 0.8008 (tttt) cc_final: 0.6694 (mptt) REVERT: A 360 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6121 (mt-10) REVERT: I 89 ASN cc_start: 0.7232 (p0) cc_final: 0.6939 (p0) REVERT: I 145 TRP cc_start: 0.9053 (m100) cc_final: 0.8591 (m100) REVERT: I 175 ASP cc_start: 0.8343 (p0) cc_final: 0.7616 (p0) REVERT: I 298 GLU cc_start: 0.7323 (pp20) cc_final: 0.7078 (pp20) REVERT: I 308 GLU cc_start: 0.7937 (pt0) cc_final: 0.7639 (pt0) REVERT: I 331 LYS cc_start: 0.8007 (tttt) cc_final: 0.6692 (mptt) REVERT: I 360 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6129 (mt-10) outliers start: 20 outliers final: 16 residues processed: 73 average time/residue: 0.1929 time to fit residues: 20.2607 Evaluate side-chains 75 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 I residue 368 LEU 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 66 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.160366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118259 restraints weight = 7905.926| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.70 r_work: 0.3311 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8302 Z= 0.197 Angle : 0.628 7.695 10978 Z= 0.314 Chirality : 0.045 0.326 1194 Planarity : 0.004 0.037 1314 Dihedral : 12.238 59.463 1638 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.49 % Allowed : 12.09 % Favored : 85.41 % 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: 1.17 (0.29), residues: 934 helix: 3.26 (0.27), residues: 334 sheet: -0.59 (0.25), residues: 408 loop : -0.40 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 36 HIS 0.004 0.001 HIS I 346 PHE 0.011 0.001 PHE A 126 TYR 0.018 0.002 TYR I 307 ARG 0.003 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.02652 ( 524) hydrogen bonds : angle 4.42311 ( 1524) covalent geometry : bond 0.00464 ( 8302) covalent geometry : angle 0.62843 (10978) *********************** 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 79 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.806 Fit side-chains REVERT: A 175 ASP cc_start: 0.8262 (p0) cc_final: 0.7588 (p0) REVERT: A 298 GLU cc_start: 0.7235 (pp20) cc_final: 0.6960 (pp20) REVERT: A 308 GLU cc_start: 0.7854 (pt0) cc_final: 0.7542 (pt0) REVERT: A 331 LYS cc_start: 0.7918 (tttt) cc_final: 0.6580 (mptt) REVERT: A 360 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6048 (mt-10) REVERT: I 175 ASP cc_start: 0.8276 (p0) cc_final: 0.7562 (p0) REVERT: I 298 GLU cc_start: 0.7227 (pp20) cc_final: 0.6954 (pp20) REVERT: I 308 GLU cc_start: 0.7853 (pt0) cc_final: 0.7536 (pt0) REVERT: I 331 LYS cc_start: 0.7920 (tttt) cc_final: 0.6580 (mptt) REVERT: I 360 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6057 (mt-10) outliers start: 20 outliers final: 16 residues processed: 71 average time/residue: 0.1982 time to fit residues: 20.1802 Evaluate side-chains 75 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 I residue 368 LEU 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 33 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.171038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124065 restraints weight = 8180.212| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.92 r_work: 0.3432 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2991 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= 0.124 Angle : 0.576 7.690 10978 Z= 0.288 Chirality : 0.043 0.306 1194 Planarity : 0.004 0.036 1314 Dihedral : 11.667 57.981 1638 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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 (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: 1.32 (0.29), residues: 934 helix: 3.39 (0.27), residues: 334 sheet: -0.50 (0.25), residues: 406 loop : -0.35 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 A 307 ARG 0.002 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.02416 ( 524) hydrogen bonds : angle 4.31161 ( 1524) covalent geometry : bond 0.00285 ( 8302) covalent geometry : angle 0.57631 (10978) *********************** 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 79 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.784 Fit side-chains REVERT: A 145 TRP cc_start: 0.9155 (m100) cc_final: 0.8698 (m100) REVERT: A 175 ASP cc_start: 0.8464 (p0) cc_final: 0.7837 (p0) REVERT: A 298 GLU cc_start: 0.7417 (pp20) cc_final: 0.7180 (pp20) REVERT: A 308 GLU cc_start: 0.8042 (pt0) cc_final: 0.7770 (pt0) REVERT: A 331 LYS cc_start: 0.8194 (tttt) cc_final: 0.6927 (mttp) REVERT: A 360 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6287 (mt-10) REVERT: I 145 TRP cc_start: 0.9152 (m100) cc_final: 0.8697 (m100) REVERT: I 175 ASP cc_start: 0.8457 (p0) cc_final: 0.7782 (p0) REVERT: I 298 GLU cc_start: 0.7409 (pp20) cc_final: 0.7172 (pp20) REVERT: I 308 GLU cc_start: 0.8037 (pt0) cc_final: 0.7764 (pt0) REVERT: I 331 LYS cc_start: 0.8190 (tttt) cc_final: 0.6921 (mttp) REVERT: I 360 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6292 (mt-10) outliers start: 22 outliers final: 16 residues processed: 73 average time/residue: 0.2259 time to fit residues: 22.8500 Evaluate side-chains 73 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 I residue 368 LEU 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: 1.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.163724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118144 restraints weight = 7933.335| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.93 r_work: 0.3435 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3045 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= 0.133 Angle : 0.577 8.101 10978 Z= 0.289 Chirality : 0.043 0.294 1194 Planarity : 0.004 0.037 1314 Dihedral : 11.360 56.613 1638 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.24 % Allowed : 11.85 % 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 (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: 1.15 (0.29), residues: 934 helix: 3.17 (0.27), residues: 346 sheet: -0.51 (0.25), residues: 406 loop : -0.77 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 A 307 ARG 0.007 0.000 ARG I 261 Details of bonding type rmsd hydrogen bonds : bond 0.02407 ( 524) hydrogen bonds : angle 4.28557 ( 1524) covalent geometry : bond 0.00309 ( 8302) covalent geometry : angle 0.57731 (10978) ********************** 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 74 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.816 Fit side-chains REVERT: A 145 TRP cc_start: 0.9112 (m100) cc_final: 0.8639 (m100) REVERT: A 175 ASP cc_start: 0.8419 (p0) cc_final: 0.7769 (p0) REVERT: A 298 GLU cc_start: 0.7381 (pp20) cc_final: 0.7117 (pp20) REVERT: A 308 GLU cc_start: 0.8014 (pt0) cc_final: 0.7720 (pt0) REVERT: A 331 LYS cc_start: 0.8106 (tttt) cc_final: 0.6829 (mttp) REVERT: A 360 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6192 (mt-10) REVERT: A 367 LEU cc_start: 0.6318 (mt) cc_final: 0.6051 (mt) REVERT: I 145 TRP cc_start: 0.9106 (m100) cc_final: 0.8634 (m100) REVERT: I 175 ASP cc_start: 0.8420 (p0) cc_final: 0.7720 (p0) REVERT: I 298 GLU cc_start: 0.7373 (pp20) cc_final: 0.7112 (pp20) REVERT: I 308 GLU cc_start: 0.8005 (pt0) cc_final: 0.7711 (pt0) REVERT: I 331 LYS cc_start: 0.8101 (tttt) cc_final: 0.6824 (mttp) REVERT: I 360 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6198 (mt-10) outliers start: 18 outliers final: 16 residues processed: 68 average time/residue: 0.2049 time to fit residues: 20.0080 Evaluate side-chains 73 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 I residue 368 LEU 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 55 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 67 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.165607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120315 restraints weight = 8013.333| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.87 r_work: 0.3440 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8302 Z= 0.136 Angle : 0.575 8.254 10978 Z= 0.288 Chirality : 0.043 0.279 1194 Planarity : 0.005 0.037 1314 Dihedral : 11.175 56.888 1638 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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 (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: 1.17 (0.29), residues: 934 helix: 3.17 (0.27), residues: 346 sheet: -0.53 (0.25), residues: 406 loop : -0.65 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS C 43 PHE 0.011 0.001 PHE A 126 TYR 0.014 0.001 TYR A 307 ARG 0.007 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.02373 ( 524) hydrogen bonds : angle 4.26135 ( 1524) covalent geometry : bond 0.00316 ( 8302) covalent geometry : angle 0.57520 (10978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4539.61 seconds wall clock time: 81 minutes 15.57 seconds (4875.57 seconds total)