Starting phenix.real_space_refine on Sat Sep 28 22:22:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/09_2024/7mqe_23944.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/09_2024/7mqe_23944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/09_2024/7mqe_23944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/09_2024/7mqe_23944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/09_2024/7mqe_23944.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/09_2024/7mqe_23944.cif" } resolution = 3.69 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10872 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 48 5.16 5 C 7752 2.51 5 N 2257 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12163 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1505 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1482 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 106 Chain: "E" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1448 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1483 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 107 Chain: "I" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1445 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 108 Chain: "K" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1467 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 100 Chain: "M" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1488 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 9, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 106 Chain: "O" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1477 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "P" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 7.94, per 1000 atoms: 0.65 Number of scatterers: 12163 At special positions: 0 Unit cell: (107.88, 117.8, 105.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 16 15.00 O 2090 8.00 N 2257 7.00 C 7752 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: 3.73 Conformation dependent library (CDL) restraints added in 2.0 seconds 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 45.5% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.838A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.739A pdb=" N ASP A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 196 Proline residue: A 187 - end of helix Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.844A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 145 through 155 removed outlier: 3.622A pdb=" N ASP C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 175 through 196 Proline residue: C 187 - end of helix Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.859A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 175 through 196 Proline residue: E 187 - end of helix Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 80 through 93 removed outlier: 3.921A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'G' and resid 175 through 196 Proline residue: G 187 - end of helix Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 80 through 93 removed outlier: 3.924A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA I 86 " --> pdb=" O ARG I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 145 through 155 Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 175 through 196 Proline residue: I 187 - end of helix Processing helix chain 'K' and resid 62 through 71 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.912A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 117 through 127 Processing helix chain 'K' and resid 145 through 155 removed outlier: 3.666A pdb=" N ASP K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 175 through 196 Proline residue: K 187 - end of helix Processing helix chain 'M' and resid 62 through 71 Processing helix chain 'M' and resid 80 through 93 removed outlier: 3.827A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 117 through 127 Processing helix chain 'M' and resid 145 through 155 removed outlier: 3.581A pdb=" N ASP M 155 " --> pdb=" O TYR M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'M' and resid 175 through 196 Proline residue: M 187 - end of helix Processing helix chain 'O' and resid 62 through 71 Processing helix chain 'O' and resid 80 through 93 removed outlier: 3.834A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA O 86 " --> pdb=" O ARG O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 117 through 127 Processing helix chain 'O' and resid 145 through 155 removed outlier: 3.534A pdb=" N ASP O 155 " --> pdb=" O TYR O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 173 Processing helix chain 'O' and resid 175 through 196 Proline residue: O 187 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.267A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.084A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.276A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.240A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 8 removed outlier: 6.458A pdb=" N GLU I 3 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL I 52 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL I 22 " --> pdb=" O ILE I 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.216A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 8 removed outlier: 6.330A pdb=" N GLU M 3 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL M 52 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 3 through 8 removed outlier: 6.412A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1767 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: 3.02 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3987 1.34 - 1.46: 2396 1.46 - 1.58: 5953 1.58 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 12424 Sorted by residual: bond pdb=" C ARG C 67 " pdb=" N LEU C 68 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.36e-02 5.41e+03 1.18e+01 bond pdb=" N VAL O 41 " pdb=" CA VAL O 41 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.20e-02 6.94e+03 8.71e+00 bond pdb=" N VAL G 128 " pdb=" CA VAL G 128 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.30e+00 bond pdb=" N VAL C 40 " pdb=" CA VAL C 40 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.14e+00 bond pdb=" N VAL C 41 " pdb=" CA VAL C 41 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.08e+00 ... (remaining 12419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15844 1.55 - 3.11: 982 3.11 - 4.66: 135 4.66 - 6.21: 23 6.21 - 7.76: 4 Bond angle restraints: 16988 Sorted by residual: angle pdb=" N GLN A 135 " pdb=" CA GLN A 135 " pdb=" C GLN A 135 " ideal model delta sigma weight residual 112.54 107.67 4.87 1.22e+00 6.72e-01 1.59e+01 angle pdb=" CA VAL G 128 " pdb=" C VAL G 128 " pdb=" O VAL G 128 " ideal model delta sigma weight residual 121.59 117.83 3.76 1.03e+00 9.43e-01 1.33e+01 angle pdb=" CA LEU C 43 " pdb=" C LEU C 43 " pdb=" O LEU C 43 " ideal model delta sigma weight residual 121.68 117.50 4.18 1.18e+00 7.18e-01 1.25e+01 angle pdb=" N GLN G 135 " pdb=" CA GLN G 135 " pdb=" C GLN G 135 " ideal model delta sigma weight residual 112.89 108.53 4.36 1.24e+00 6.50e-01 1.23e+01 angle pdb=" CA LEU O 43 " pdb=" C LEU O 43 " pdb=" O LEU O 43 " ideal model delta sigma weight residual 121.46 117.55 3.91 1.17e+00 7.31e-01 1.12e+01 ... (remaining 16983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 6884 18.08 - 36.16: 339 36.16 - 54.24: 83 54.24 - 72.33: 57 72.33 - 90.41: 19 Dihedral angle restraints: 7382 sinusoidal: 2634 harmonic: 4748 Sorted by residual: dihedral pdb=" CA GLN M 134 " pdb=" C GLN M 134 " pdb=" N GLN M 135 " pdb=" CA GLN M 135 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PHE O 78 " pdb=" C PHE O 78 " pdb=" N HIS O 79 " pdb=" CA HIS O 79 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE I 78 " pdb=" C PHE I 78 " pdb=" N HIS I 79 " pdb=" CA HIS I 79 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1384 0.055 - 0.110: 540 0.110 - 0.164: 121 0.164 - 0.219: 12 0.219 - 0.274: 7 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CA LEU C 38 " pdb=" N LEU C 38 " pdb=" C LEU C 38 " pdb=" CB LEU C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA LEU O 38 " pdb=" N LEU O 38 " pdb=" C LEU O 38 " pdb=" CB LEU O 38 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA VAL O 41 " pdb=" N VAL O 41 " pdb=" C VAL O 41 " pdb=" CB VAL O 41 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2061 not shown) Planarity restraints: 2095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA M 153 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ALA M 153 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA M 153 " -0.013 2.00e-02 2.50e+03 pdb=" N SER M 154 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 37 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C ARG C 37 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG C 37 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU C 38 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG O 37 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ARG O 37 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG O 37 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU O 38 " 0.011 2.00e-02 2.50e+03 ... (remaining 2092 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3527 2.83 - 3.34: 10699 3.34 - 3.86: 19724 3.86 - 4.38: 22813 4.38 - 4.90: 40034 Nonbonded interactions: 96797 Sorted by model distance: nonbonded pdb=" NH1 ARG I 82 " pdb=" OD2 ASP I 193 " model vdw 2.308 3.120 nonbonded pdb=" OH TYR C 112 " pdb=" OE2 GLU C 124 " model vdw 2.327 3.040 nonbonded pdb=" OG1 THR K 26 " pdb=" OD1 ASP K 84 " model vdw 2.428 3.040 nonbonded pdb=" OG1 THR G 26 " pdb=" OD1 ASP G 84 " model vdw 2.435 3.040 nonbonded pdb=" O LYS I 103 " pdb=" OG SER I 106 " model vdw 2.442 3.040 ... (remaining 96792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 46 or (resid 47 and (name N or nam \ e CA or name C or name O or name CB )) or resid 48 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 105 or (resid 106 and (name N or name CA or name C or name O o \ r name CB )) or resid 107 through 114 or (resid 115 and (name N or name CA or na \ me C or name O or name CB )) or resid 116 through 118 or (resid 119 through 120 \ and (name N or name CA or name C or name O or name CB )) or resid 121 through 12 \ 3 or (resid 124 and (name N or name CA or name C or name O or name CB )) or resi \ d 125 through 126 or (resid 127 through 131 and (name N or name CA or name C or \ name O or name CB )) or resid 136 through 148 or (resid 149 through 150 and (nam \ e N or name CA or name C or name O or name CB )) or resid 151 through 163 or (re \ sid 164 through 165 and (name N or name CA or name C or name O or name CB )) or \ resid 166 through 176 or (resid 177 and (name N or name CA or name C or name O o \ r name CB )) or resid 178 through 200 or (resid 201 and (name N or name CA or na \ me C or name O or name CB )) or resid 202 through 206)) selection = (chain 'C' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 66 or (resid 67 and (name N or name \ CA or name C or name O or name CB )) or resid 68 through 70 or (resid 71 through \ 73 and (name N or name CA or name C or name O or name CB )) or resid 74 through \ 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or res \ id 95 through 119 or (resid 120 and (name N or name CA or name C or name O or na \ me CB )) or resid 121 through 123 or (resid 124 and (name N or name CA or name C \ or name O or name CB )) or resid 125 through 131 or resid 136 through 148 or (r \ esid 149 through 150 and (name N or name CA or name C or name O or name CB )) or \ resid 151 through 164 or (resid 165 and (name N or name CA or name C or name O \ or name CB )) or resid 166 or (resid 167 through 168 and (name N or name CA or n \ ame C or name O or name CB )) or resid 169 through 176 or (resid 177 and (name N \ or name CA or name C or name O or name CB )) or resid 178 through 179 or (resid \ 180 through 181 and (name N or name CA or name C or name O or name CB )) or res \ id 182 through 206)) selection = (chain 'E' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 or (resid 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 60 or (r \ esid 61 through 62 and (name N or name CA or name C or name O or name CB )) or r \ esid 63 through 66 or (resid 67 and (name N or name CA or name C or name O or na \ me CB )) or resid 68 through 105 or (resid 106 and (name N or name CA or name C \ or name O or name CB )) or resid 107 through 154 or (resid 155 and (name N or na \ me CA or name C or name O or name CB )) or resid 156 through 163 or (resid 164 t \ hrough 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ through 172 or (resid 173 through 174 and (name N or name CA or name C or name \ O or name CB )) or resid 175 through 176 or (resid 177 and (name N or name CA or \ name C or name O or name CB )) or resid 178 through 179 or (resid 180 through 1 \ 81 and (name N or name CA or name C or name O or name CB )) or resid 182 through \ 200 or (resid 201 and (name N or name CA or name C or name O or name CB )) or r \ esid 202 through 206)) selection = (chain 'G' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 63 or (resid 64 and (na \ me N or name CA or name C or name O or name CB )) or resid 65 through 105 or (re \ sid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 th \ rough 114 or (resid 115 and (name N or name CA or name C or name O or name CB )) \ or resid 116 through 127 or (resid 128 through 131 and (name N or name CA or na \ me C or name O or name CB )) or resid 136 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 4 or (resid 155 and (name N or name CA or name C or name O or name CB )) or resi \ d 156 through 164 or (resid 165 and (name N or name CA or name C or name O or na \ me CB )) or resid 166 or (resid 167 through 168 and (name N or name CA or name C \ or name O or name CB )) or resid 169 through 172 or (resid 173 through 174 and \ (name N or name CA or name C or name O or name CB )) or resid 175 through 206)) selection = (chain 'I' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 27 or (resid 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 66 or (res \ id 67 and (name N or name CA or name C or name O or name CB )) or resid 68 throu \ gh 69 or (resid 70 through 73 and (name N or name CA or name C or name O or name \ CB )) or resid 74 through 93 or (resid 94 and (name N or name CA or name C or n \ ame O or name CB )) or resid 95 through 105 or (resid 106 and (name N or name CA \ or name C or name O or name CB )) or resid 107 through 119 or (resid 120 and (n \ ame N or name CA or name C or name O or name CB )) or resid 121 through 128 or ( \ resid 129 through 138 and (name N or name CA or name C or name O or name CB )) o \ r resid 139 through 154 or (resid 155 and (name N or name CA or name C or name O \ or name CB )) or resid 156 through 176 or (resid 177 and (name N or name CA or \ name C or name O or name CB )) or resid 178 through 179 or (resid 180 through 18 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 182 through \ 206)) selection = (chain 'K' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 56 or (resid 57 and (name N or nam \ e CA or name C or name O or name CB )) or resid 58 through 60 or (resid 61 throu \ gh 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 105 or (resid 106 and (name N or name CA or name C or name O or name CB )) \ or resid 107 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 118 or (resid 119 through 120 and (name N o \ r name CA or name C or name O or name CB )) or resid 121 through 127 or (resid 1 \ 28 through 131 and (name N or name CA or name C or name O or name CB )) or (resi \ d 136 through 138 and (name N or name CA or name C or name O or name CB )) or re \ sid 139 through 148 or (resid 149 through 150 and (name N or name CA or name C o \ r name O or name CB )) or resid 151 through 163 or (resid 164 through 165 and (n \ ame N or name CA or name C or name O or name CB )) or resid 166 through 172 or ( \ resid 173 through 174 and (name N or name CA or name C or name O or name CB )) o \ r resid 175 through 176 or (resid 177 and (name N or name CA or name C or name O \ or name CB )) or resid 178 through 206)) selection = (chain 'M' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 or (resid 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 69 or (resid 70 through 73 and (name N or name CA or name C or \ name O or name CB )) or resid 74 through 93 or (resid 94 and (name N or name CA \ or name C or name O or name CB )) or resid 95 through 105 or (resid 106 and (na \ me N or name CA or name C or name O or name CB )) or resid 107 through 114 or (r \ esid 115 and (name N or name CA or name C or name O or name CB )) or resid 116 t \ hrough 123 or (resid 124 and (name N or name CA or name C or name O or name CB ) \ ) or resid 125 through 127 or (resid 128 through 131 and (name N or name CA or n \ ame C or name O or name CB )) or resid 136 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 1 \ 64 or (resid 165 and (name N or name CA or name C or name O or name CB )) or res \ id 166 through 176 or (resid 177 and (name N or name CA or name C or name O or n \ ame CB )) or resid 178 through 179 or (resid 180 through 181 and (name N or name \ CA or name C or name O or name CB )) or resid 182 through 200 or (resid 201 and \ (name N or name CA or name C or name O or name CB )) or resid 202 through 206)) \ selection = (chain 'O' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB )) or resid 58 through 60 or (resid 61 through 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 66 or (resid \ 67 and (name N or name CA or name C or name O or name CB )) or resid 68 through \ 69 or (resid 70 through 73 and (name N or name CA or name C or name O or name C \ B )) or resid 74 through 105 or (resid 106 and (name N or name CA or name C or n \ ame O or name CB )) or resid 107 through 118 or (resid 119 through 120 and (name \ N or name CA or name C or name O or name CB )) or resid 121 through 123 or (res \ id 124 and (name N or name CA or name C or name O or name CB )) or resid 125 thr \ ough 131 or resid 136 through 148 or (resid 149 through 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 164 or (resid 165 and \ (name N or name CA or name C or name O or name CB )) or resid 166 or (resid 167 \ through 168 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 9 through 176 or (resid 177 and (name N or name CA or name C or name O or name C \ B )) or resid 178 through 179 or (resid 180 through 181 and (name N or name CA o \ r name C or name O or name CB )) or resid 182 through 206)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } 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 group one per residue 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.610 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.008 0.071 12424 Z= 0.545 Angle : 0.840 7.763 16988 Z= 0.510 Chirality : 0.059 0.274 2064 Planarity : 0.005 0.032 2095 Dihedral : 14.658 90.408 4284 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.77 % Allowed : 0.68 % Favored : 98.55 % 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: 0.67 (0.20), residues: 1607 helix: 0.34 (0.18), residues: 726 sheet: 0.22 (0.24), residues: 253 loop : 0.98 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 197 HIS 0.007 0.001 HIS E 205 PHE 0.021 0.003 PHE M 78 TYR 0.026 0.003 TYR E 17 ARG 0.013 0.002 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 187 time to evaluate : 1.306 Fit side-chains REVERT: A 201 ASP cc_start: 0.7958 (t0) cc_final: 0.7452 (t0) REVERT: C 25 ASP cc_start: 0.8187 (t70) cc_final: 0.7636 (t0) REVERT: E 16 ASN cc_start: 0.7290 (m-40) cc_final: 0.7059 (m-40) REVERT: E 27 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7898 (mm-30) REVERT: E 42 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: E 201 ASP cc_start: 0.7573 (t0) cc_final: 0.7211 (t0) REVERT: G 42 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8355 (mt0) REVERT: I 42 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8017 (mt0) REVERT: I 67 ARG cc_start: 0.7067 (ttp-110) cc_final: 0.6850 (ttp80) REVERT: I 95 MET cc_start: 0.7721 (tpp) cc_final: 0.7496 (tpp) REVERT: K 42 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: M 201 ASP cc_start: 0.7791 (t0) cc_final: 0.7275 (t0) REVERT: O 25 ASP cc_start: 0.8280 (t70) cc_final: 0.7736 (t0) REVERT: O 188 MET cc_start: 0.7339 (mmm) cc_final: 0.6787 (tpp) outliers start: 8 outliers final: 0 residues processed: 195 average time/residue: 0.2280 time to fit residues: 64.8116 Evaluate side-chains 161 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain K residue 42 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN M 8 GLN M 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 12424 Z= 0.171 Angle : 0.468 7.370 16988 Z= 0.251 Chirality : 0.044 0.128 2064 Planarity : 0.003 0.024 2095 Dihedral : 11.623 84.578 2030 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.68 % Allowed : 4.82 % Favored : 94.50 % 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: 1.86 (0.22), residues: 1607 helix: 1.74 (0.20), residues: 729 sheet: 0.83 (0.25), residues: 254 loop : 1.00 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 197 HIS 0.002 0.000 HIS C 160 PHE 0.016 0.001 PHE C 78 TYR 0.009 0.001 TYR M 17 ARG 0.005 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 1.306 Fit side-chains REVERT: A 201 ASP cc_start: 0.7888 (t0) cc_final: 0.7444 (t0) REVERT: C 25 ASP cc_start: 0.8006 (t70) cc_final: 0.7690 (t0) REVERT: C 71 ASP cc_start: 0.6804 (t0) cc_final: 0.6458 (t0) REVERT: C 188 MET cc_start: 0.7636 (tpp) cc_final: 0.7144 (tpp) REVERT: E 25 ASP cc_start: 0.7751 (t0) cc_final: 0.7466 (t0) REVERT: E 201 ASP cc_start: 0.7224 (t0) cc_final: 0.6851 (t0) REVERT: G 27 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7645 (mm-30) REVERT: G 157 LEU cc_start: 0.8129 (mt) cc_final: 0.7819 (mt) REVERT: I 25 ASP cc_start: 0.7874 (t70) cc_final: 0.7497 (t0) REVERT: I 95 MET cc_start: 0.8149 (tpp) cc_final: 0.7784 (tpp) REVERT: I 120 GLU cc_start: 0.8448 (tp30) cc_final: 0.8237 (tp30) REVERT: K 157 LEU cc_start: 0.8259 (mt) cc_final: 0.8058 (mt) REVERT: K 164 ASP cc_start: 0.7188 (m-30) cc_final: 0.6718 (m-30) REVERT: M 188 MET cc_start: 0.7966 (tpp) cc_final: 0.7710 (mmm) REVERT: O 188 MET cc_start: 0.7512 (mmm) cc_final: 0.6707 (tpp) outliers start: 7 outliers final: 2 residues processed: 178 average time/residue: 0.2178 time to fit residues: 57.4641 Evaluate side-chains 150 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 32 GLN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN C 54 GLN C 205 HIS E 32 GLN E 42 GLN G 8 GLN I 42 GLN ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 ASN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12424 Z= 0.390 Angle : 0.550 7.869 16988 Z= 0.291 Chirality : 0.048 0.134 2064 Planarity : 0.004 0.045 2095 Dihedral : 11.191 63.926 2018 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.25 % Allowed : 6.85 % Favored : 91.90 % 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: 1.34 (0.21), residues: 1607 helix: 1.30 (0.20), residues: 729 sheet: 0.86 (0.27), residues: 254 loop : 0.60 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 197 HIS 0.005 0.001 HIS M 116 PHE 0.017 0.002 PHE C 78 TYR 0.014 0.002 TYR C 151 ARG 0.005 0.001 ARG I 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 1.435 Fit side-chains REVERT: A 124 GLU cc_start: 0.8192 (tt0) cc_final: 0.7628 (tt0) REVERT: C 25 ASP cc_start: 0.8092 (t70) cc_final: 0.7710 (t0) REVERT: C 27 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7698 (mm-30) REVERT: C 95 MET cc_start: 0.7896 (tpp) cc_final: 0.7653 (tpp) REVERT: C 188 MET cc_start: 0.7826 (tpp) cc_final: 0.7230 (tpp) REVERT: E 95 MET cc_start: 0.8484 (tpp) cc_final: 0.8242 (tpt) REVERT: G 27 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8023 (mm-30) REVERT: G 157 LEU cc_start: 0.8245 (mt) cc_final: 0.7989 (mt) REVERT: I 95 MET cc_start: 0.8376 (tpp) cc_final: 0.7801 (tpp) REVERT: K 64 ASN cc_start: 0.8533 (m-40) cc_final: 0.8308 (m-40) REVERT: M 16 ASN cc_start: 0.7508 (m-40) cc_final: 0.7238 (m-40) REVERT: O 8 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8187 (mp10) REVERT: O 188 MET cc_start: 0.7538 (mmm) cc_final: 0.6897 (tpp) outliers start: 13 outliers final: 13 residues processed: 158 average time/residue: 0.2138 time to fit residues: 50.9128 Evaluate side-chains 162 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 122 CYS Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN C 8 GLN C 54 GLN I 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 12424 Z= 0.121 Angle : 0.397 8.170 16988 Z= 0.214 Chirality : 0.042 0.123 2064 Planarity : 0.003 0.024 2095 Dihedral : 10.781 63.867 2018 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.87 % Allowed : 7.71 % Favored : 91.42 % 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: 1.61 (0.22), residues: 1607 helix: 1.61 (0.20), residues: 730 sheet: 1.06 (0.27), residues: 257 loop : 0.58 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP K 139 HIS 0.004 0.000 HIS C 7 PHE 0.013 0.001 PHE O 78 TYR 0.017 0.001 TYR K 151 ARG 0.003 0.000 ARG I 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.448 Fit side-chains REVERT: A 201 ASP cc_start: 0.8291 (t0) cc_final: 0.7760 (t0) REVERT: A 206 SER cc_start: 0.6372 (p) cc_final: 0.6018 (t) REVERT: C 71 ASP cc_start: 0.7076 (t0) cc_final: 0.6810 (t0) REVERT: C 188 MET cc_start: 0.7714 (tpp) cc_final: 0.7195 (tpp) REVERT: E 25 ASP cc_start: 0.7668 (t70) cc_final: 0.7371 (t0) REVERT: E 95 MET cc_start: 0.8532 (tpp) cc_final: 0.8286 (tpt) REVERT: E 201 ASP cc_start: 0.7096 (t0) cc_final: 0.6643 (t0) REVERT: G 27 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7689 (mm-30) REVERT: G 157 LEU cc_start: 0.8063 (mt) cc_final: 0.7793 (mt) REVERT: I 95 MET cc_start: 0.8333 (tpp) cc_final: 0.7925 (tpp) REVERT: K 64 ASN cc_start: 0.8515 (m-40) cc_final: 0.8293 (m-40) REVERT: M 16 ASN cc_start: 0.7391 (m-40) cc_final: 0.7035 (m-40) REVERT: M 17 TYR cc_start: 0.7615 (m-80) cc_final: 0.7362 (m-80) REVERT: M 201 ASP cc_start: 0.8024 (t0) cc_final: 0.7261 (t0) REVERT: O 67 ARG cc_start: 0.7318 (mtm180) cc_final: 0.7016 (ttp-110) REVERT: O 188 MET cc_start: 0.7426 (mmm) cc_final: 0.6831 (tpp) REVERT: O 191 ASN cc_start: 0.8625 (t0) cc_final: 0.8388 (t0) outliers start: 9 outliers final: 6 residues processed: 163 average time/residue: 0.2135 time to fit residues: 53.1251 Evaluate side-chains 151 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 122 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 115 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 0.0020 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN C 54 GLN I 32 GLN O 8 GLN O 54 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12424 Z= 0.158 Angle : 0.406 8.513 16988 Z= 0.217 Chirality : 0.043 0.121 2064 Planarity : 0.003 0.024 2095 Dihedral : 10.660 63.876 2018 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.25 % Allowed : 8.10 % Favored : 90.65 % 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: 1.63 (0.22), residues: 1607 helix: 1.57 (0.20), residues: 732 sheet: 1.25 (0.27), residues: 257 loop : 0.57 (0.28), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 139 HIS 0.005 0.000 HIS C 7 PHE 0.012 0.001 PHE O 78 TYR 0.009 0.001 TYR A 151 ARG 0.003 0.000 ARG I 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.444 Fit side-chains REVERT: A 122 CYS cc_start: 0.7866 (m) cc_final: 0.7632 (m) REVERT: A 201 ASP cc_start: 0.8186 (t0) cc_final: 0.7486 (t0) REVERT: A 206 SER cc_start: 0.6428 (p) cc_final: 0.6051 (t) REVERT: C 71 ASP cc_start: 0.7107 (t0) cc_final: 0.6835 (t0) REVERT: C 188 MET cc_start: 0.7986 (tpp) cc_final: 0.7540 (tpp) REVERT: E 25 ASP cc_start: 0.7801 (t70) cc_final: 0.7532 (t0) REVERT: E 95 MET cc_start: 0.8524 (tpp) cc_final: 0.8207 (tpp) REVERT: E 201 ASP cc_start: 0.7006 (t0) cc_final: 0.6535 (t0) REVERT: G 27 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7687 (mm-30) REVERT: G 157 LEU cc_start: 0.8046 (mt) cc_final: 0.7780 (mt) REVERT: I 95 MET cc_start: 0.8374 (tpp) cc_final: 0.7944 (tpp) REVERT: M 16 ASN cc_start: 0.7374 (m-40) cc_final: 0.7037 (m-40) REVERT: M 17 TYR cc_start: 0.7657 (m-80) cc_final: 0.7342 (m-80) REVERT: M 124 GLU cc_start: 0.7901 (tt0) cc_final: 0.7577 (tm-30) REVERT: M 201 ASP cc_start: 0.7994 (t0) cc_final: 0.7278 (t0) REVERT: O 8 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8119 (mp10) REVERT: O 67 ARG cc_start: 0.7303 (mtm180) cc_final: 0.7014 (ttp-110) REVERT: O 188 MET cc_start: 0.7558 (mmm) cc_final: 0.6976 (tpp) REVERT: O 191 ASN cc_start: 0.8654 (t0) cc_final: 0.8428 (t0) outliers start: 13 outliers final: 10 residues processed: 158 average time/residue: 0.1992 time to fit residues: 48.5360 Evaluate side-chains 158 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN C 54 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12424 Z= 0.269 Angle : 0.455 8.540 16988 Z= 0.241 Chirality : 0.044 0.127 2064 Planarity : 0.003 0.028 2095 Dihedral : 10.764 63.913 2018 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.64 % Allowed : 8.39 % Favored : 89.97 % 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: 1.43 (0.22), residues: 1607 helix: 1.38 (0.20), residues: 732 sheet: 1.21 (0.28), residues: 257 loop : 0.47 (0.28), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 139 HIS 0.006 0.001 HIS C 7 PHE 0.015 0.001 PHE C 78 TYR 0.013 0.001 TYR A 151 ARG 0.003 0.000 ARG I 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.349 Fit side-chains REVERT: A 201 ASP cc_start: 0.8133 (t0) cc_final: 0.7422 (t0) REVERT: C 188 MET cc_start: 0.8059 (tpp) cc_final: 0.7580 (tpp) REVERT: E 25 ASP cc_start: 0.7841 (t70) cc_final: 0.7551 (t0) REVERT: E 95 MET cc_start: 0.8423 (tpp) cc_final: 0.8154 (tpt) REVERT: G 27 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7801 (mm-30) REVERT: G 157 LEU cc_start: 0.8125 (mt) cc_final: 0.7851 (mt) REVERT: I 95 MET cc_start: 0.8410 (tpp) cc_final: 0.7958 (tpp) REVERT: K 27 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7147 (mm-30) REVERT: M 124 GLU cc_start: 0.7970 (tt0) cc_final: 0.7603 (tm-30) REVERT: M 201 ASP cc_start: 0.8152 (t0) cc_final: 0.7467 (t0) REVERT: O 8 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8088 (mp10) REVERT: O 67 ARG cc_start: 0.7350 (mtm180) cc_final: 0.7051 (ttp-110) REVERT: O 106 SER cc_start: 0.9296 (t) cc_final: 0.8999 (t) REVERT: O 188 MET cc_start: 0.7513 (mmm) cc_final: 0.6934 (tpp) outliers start: 17 outliers final: 13 residues processed: 145 average time/residue: 0.1979 time to fit residues: 44.4718 Evaluate side-chains 147 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain I residue 129 ASN Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN C 54 GLN E 42 GLN I 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 12424 Z= 0.490 Angle : 0.578 8.357 16988 Z= 0.304 Chirality : 0.049 0.139 2064 Planarity : 0.004 0.038 2095 Dihedral : 11.122 63.979 2018 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.74 % Allowed : 8.39 % Favored : 89.87 % 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: 0.80 (0.21), residues: 1607 helix: 0.94 (0.19), residues: 730 sheet: 0.75 (0.29), residues: 257 loop : 0.12 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 139 HIS 0.006 0.001 HIS A 116 PHE 0.017 0.002 PHE C 78 TYR 0.016 0.002 TYR A 151 ARG 0.005 0.001 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.276 Fit side-chains REVERT: C 188 MET cc_start: 0.7927 (tpp) cc_final: 0.7313 (tpp) REVERT: E 25 ASP cc_start: 0.7860 (t70) cc_final: 0.7544 (t0) REVERT: G 27 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7979 (mm-30) REVERT: G 157 LEU cc_start: 0.8266 (mt) cc_final: 0.8028 (mt) REVERT: I 95 MET cc_start: 0.8461 (tpp) cc_final: 0.7847 (tpp) REVERT: M 70 SER cc_start: 0.8736 (m) cc_final: 0.8218 (p) REVERT: O 8 GLN cc_start: 0.8523 (mm-40) cc_final: 0.7985 (mp10) REVERT: O 67 ARG cc_start: 0.7375 (mtm180) cc_final: 0.7084 (ttp-110) REVERT: O 154 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8604 (t) REVERT: O 188 MET cc_start: 0.7537 (mmm) cc_final: 0.6911 (tpp) outliers start: 18 outliers final: 12 residues processed: 154 average time/residue: 0.1916 time to fit residues: 45.5667 Evaluate side-chains 158 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 16 ASN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12424 Z= 0.189 Angle : 0.426 8.809 16988 Z= 0.228 Chirality : 0.044 0.263 2064 Planarity : 0.003 0.026 2095 Dihedral : 10.767 63.883 2018 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.96 % Allowed : 9.64 % Favored : 89.39 % 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 (0.22), residues: 1607 helix: 1.26 (0.20), residues: 731 sheet: 0.93 (0.29), residues: 257 loop : 0.23 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 139 HIS 0.002 0.001 HIS E 205 PHE 0.014 0.001 PHE O 78 TYR 0.022 0.001 TYR A 151 ARG 0.003 0.000 ARG I 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.277 Fit side-chains REVERT: A 124 GLU cc_start: 0.7916 (tt0) cc_final: 0.7598 (tm-30) REVERT: A 135 GLN cc_start: 0.5840 (tt0) cc_final: 0.5185 (pt0) REVERT: C 8 GLN cc_start: 0.8384 (mp10) cc_final: 0.8121 (mp10) REVERT: C 188 MET cc_start: 0.8030 (tpp) cc_final: 0.7575 (tpp) REVERT: E 25 ASP cc_start: 0.7633 (t70) cc_final: 0.7428 (t0) REVERT: G 27 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7833 (mm-30) REVERT: G 157 LEU cc_start: 0.8238 (mt) cc_final: 0.7981 (mt) REVERT: K 27 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7028 (mm-30) REVERT: M 17 TYR cc_start: 0.7906 (m-80) cc_final: 0.7651 (m-80) REVERT: M 124 GLU cc_start: 0.8005 (tt0) cc_final: 0.7583 (tm-30) REVERT: O 67 ARG cc_start: 0.7352 (mtm180) cc_final: 0.7116 (ttp-110) REVERT: O 106 SER cc_start: 0.9280 (t) cc_final: 0.9013 (t) REVERT: O 148 GLN cc_start: 0.8156 (mt0) cc_final: 0.7923 (mt0) REVERT: O 154 SER cc_start: 0.8829 (p) cc_final: 0.8514 (t) REVERT: O 188 MET cc_start: 0.7560 (mmm) cc_final: 0.6969 (tpp) REVERT: O 191 ASN cc_start: 0.8703 (t0) cc_final: 0.8454 (t0) outliers start: 10 outliers final: 9 residues processed: 155 average time/residue: 0.1935 time to fit residues: 46.4081 Evaluate side-chains 152 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain M residue 16 ASN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN O 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 12424 Z= 0.452 Angle : 0.557 8.833 16988 Z= 0.292 Chirality : 0.049 0.250 2064 Planarity : 0.004 0.033 2095 Dihedral : 10.951 63.975 2018 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.16 % Allowed : 9.84 % Favored : 89.01 % 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: 0.67 (0.21), residues: 1607 helix: 0.92 (0.19), residues: 730 sheet: 0.62 (0.29), residues: 257 loop : -0.05 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 139 HIS 0.006 0.001 HIS M 116 PHE 0.017 0.002 PHE C 78 TYR 0.018 0.002 TYR A 151 ARG 0.004 0.001 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 1.432 Fit side-chains REVERT: A 135 GLN cc_start: 0.6150 (tt0) cc_final: 0.4981 (pp30) REVERT: C 8 GLN cc_start: 0.8480 (mp10) cc_final: 0.8227 (mp10) REVERT: C 188 MET cc_start: 0.7945 (tpp) cc_final: 0.7354 (tpp) REVERT: E 25 ASP cc_start: 0.7777 (t70) cc_final: 0.7514 (t0) REVERT: G 27 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7957 (mm-30) REVERT: I 95 MET cc_start: 0.8502 (tpp) cc_final: 0.8035 (tpp) REVERT: M 70 SER cc_start: 0.8720 (m) cc_final: 0.8215 (p) REVERT: O 8 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7894 (mp10) REVERT: O 67 ARG cc_start: 0.7410 (mtm180) cc_final: 0.7138 (ttp-110) REVERT: O 154 SER cc_start: 0.8856 (p) cc_final: 0.8566 (t) REVERT: O 188 MET cc_start: 0.7670 (mmm) cc_final: 0.6952 (tpp) outliers start: 12 outliers final: 10 residues processed: 153 average time/residue: 0.1969 time to fit residues: 46.6652 Evaluate side-chains 153 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain M residue 16 ASN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 0.0370 chunk 105 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12424 Z= 0.132 Angle : 0.411 8.926 16988 Z= 0.220 Chirality : 0.042 0.184 2064 Planarity : 0.003 0.026 2095 Dihedral : 10.468 63.877 2018 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.58 % Allowed : 10.32 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.22), residues: 1607 helix: 1.38 (0.20), residues: 731 sheet: 0.94 (0.29), residues: 257 loop : 0.12 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 139 HIS 0.002 0.000 HIS E 205 PHE 0.013 0.001 PHE O 78 TYR 0.024 0.001 TYR A 151 ARG 0.003 0.000 ARG I 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 1.432 Fit side-chains REVERT: A 124 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 135 GLN cc_start: 0.5750 (tt0) cc_final: 0.5241 (pt0) REVERT: C 8 GLN cc_start: 0.8457 (mp10) cc_final: 0.8137 (mp10) REVERT: C 188 MET cc_start: 0.8058 (tpp) cc_final: 0.7586 (tpp) REVERT: G 27 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7673 (mm-30) REVERT: I 95 MET cc_start: 0.8552 (tpp) cc_final: 0.8124 (tpt) REVERT: K 27 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6910 (mm-30) REVERT: M 124 GLU cc_start: 0.7929 (tt0) cc_final: 0.7513 (tm-30) REVERT: O 67 ARG cc_start: 0.7371 (mtm180) cc_final: 0.7151 (ttp-110) REVERT: O 106 SER cc_start: 0.9295 (t) cc_final: 0.9034 (t) REVERT: O 148 GLN cc_start: 0.8148 (mt0) cc_final: 0.7912 (mt0) REVERT: O 154 SER cc_start: 0.8830 (p) cc_final: 0.8446 (t) REVERT: O 188 MET cc_start: 0.7628 (mmm) cc_final: 0.7085 (tpp) REVERT: O 191 ASN cc_start: 0.8606 (t0) cc_final: 0.8378 (t0) outliers start: 6 outliers final: 6 residues processed: 146 average time/residue: 0.2114 time to fit residues: 47.4146 Evaluate side-chains 146 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.097439 restraints weight = 16543.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.099074 restraints weight = 12598.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.100388 restraints weight = 10249.510| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12424 Z= 0.186 Angle : 0.426 9.091 16988 Z= 0.226 Chirality : 0.043 0.171 2064 Planarity : 0.003 0.027 2095 Dihedral : 10.480 63.895 2018 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.87 % Allowed : 10.32 % Favored : 88.81 % 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: 1.22 (0.22), residues: 1607 helix: 1.42 (0.20), residues: 731 sheet: 0.96 (0.29), residues: 257 loop : 0.14 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 139 HIS 0.002 0.001 HIS A 79 PHE 0.013 0.001 PHE O 78 TYR 0.032 0.001 TYR M 151 ARG 0.003 0.000 ARG I 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1935.65 seconds wall clock time: 35 minutes 46.04 seconds (2146.04 seconds total)