Starting phenix.real_space_refine on Sun Sep 29 05:13:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqg_23946/09_2024/7mqg_23946.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqg_23946/09_2024/7mqg_23946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqg_23946/09_2024/7mqg_23946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqg_23946/09_2024/7mqg_23946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqg_23946/09_2024/7mqg_23946.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqg_23946/09_2024/7mqg_23946.cif" } resolution = 3.25 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= 0.018 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 11321 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 8017 2.51 5 N 2313 2.21 5 O 2276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12670 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1525 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1538 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 61 Chain: "G" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1541 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 64 Chain: "I" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 69 Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1536 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 72 Chain: "M" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1543 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 66 Chain: "O" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1534 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 75 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: 7.92, per 1000 atoms: 0.63 Number of scatterers: 12670 At special positions: 0 Unit cell: (105.4, 117.8, 110.36, 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 2276 8.00 N 2313 7.00 C 8017 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 45.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.922A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.526A 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: 3.629A 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: 4.047A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.549A 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 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 62 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 4.003A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.625A 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 removed outlier: 3.554A pdb=" N ASP E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) 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: 4.005A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.599A 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 removed outlier: 3.532A pdb=" N ASP G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) 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: 3.973A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.614A 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 removed outlier: 3.619A pdb=" N ASP I 155 " --> pdb=" O TYR I 151 " (cutoff:3.500A) 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: 3.969A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.823A 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: 3.973A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.613A 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: 3.612A 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: 3.992A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.562A 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 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 3 through 8 Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.260A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.823A 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: 6.318A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA E 23 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.303A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 8 removed outlier: 6.701A pdb=" N GLU I 3 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL I 52 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 8 removed outlier: 6.666A pdb=" N GLU K 3 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL K 52 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL K 22 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 8 removed outlier: 6.620A pdb=" N GLU M 3 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL M 52 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.764A 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: 6.580A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1755 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: 3.32 Time building geometry restraints manager: 3.76 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: 4206 1.34 - 1.46: 1958 1.46 - 1.57: 6682 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 12934 Sorted by residual: bond pdb=" N GLU O 27 " pdb=" CA GLU O 27 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.26e-02 6.30e+03 7.59e+00 bond pdb=" N TYR A 151 " pdb=" CA TYR A 151 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.64e+00 bond pdb=" CG LEU M 68 " pdb=" CD1 LEU M 68 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CG ARG M 169 " pdb=" CD ARG M 169 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" CA GLU O 27 " pdb=" C GLU O 27 " ideal model delta sigma weight residual 1.520 1.539 -0.019 1.20e-02 6.94e+03 2.43e+00 ... (remaining 12929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 17361 2.31 - 4.63: 271 4.63 - 6.94: 31 6.94 - 9.25: 6 9.25 - 11.57: 3 Bond angle restraints: 17672 Sorted by residual: angle pdb=" C LYS A 132 " pdb=" N GLN A 133 " pdb=" CA GLN A 133 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CB MET E 188 " pdb=" CG MET E 188 " pdb=" SD MET E 188 " ideal model delta sigma weight residual 112.70 101.13 11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C ASP E 138 " pdb=" N TRP E 139 " pdb=" CA TRP E 139 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" CB LYS O 119 " pdb=" CG LYS O 119 " pdb=" CD LYS O 119 " ideal model delta sigma weight residual 111.30 119.03 -7.73 2.30e+00 1.89e-01 1.13e+01 angle pdb=" CB MET I 95 " pdb=" CG MET I 95 " pdb=" SD MET I 95 " ideal model delta sigma weight residual 112.70 122.37 -9.67 3.00e+00 1.11e-01 1.04e+01 ... (remaining 17667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 7162 17.19 - 34.39: 404 34.39 - 51.58: 98 51.58 - 68.78: 51 68.78 - 85.97: 9 Dihedral angle restraints: 7724 sinusoidal: 2940 harmonic: 4784 Sorted by residual: 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 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+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 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA PHE K 78 " pdb=" C PHE K 78 " pdb=" N HIS K 79 " pdb=" CA HIS K 79 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 7721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1250 0.043 - 0.085: 621 0.085 - 0.128: 223 0.128 - 0.171: 30 0.171 - 0.214: 3 Chirality restraints: 2127 Sorted by residual: chirality pdb=" CG LEU M 14 " pdb=" CB LEU M 14 " pdb=" CD1 LEU M 14 " pdb=" CD2 LEU M 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ARG C 72 " pdb=" N ARG C 72 " pdb=" C ARG C 72 " pdb=" CB ARG C 72 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU E 125 " pdb=" CB LEU E 125 " pdb=" CD1 LEU E 125 " pdb=" CD2 LEU E 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 2124 not shown) Planarity restraints: 2203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA M 153 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+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 THR O 26 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C THR O 26 " 0.033 2.00e-02 2.50e+03 pdb=" O THR O 26 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU O 27 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 83 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C PHE C 83 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE C 83 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP C 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 2200 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 875 2.73 - 3.27: 11929 3.27 - 3.82: 20435 3.82 - 4.36: 26259 4.36 - 4.90: 43967 Nonbonded interactions: 103465 Sorted by model distance: nonbonded pdb=" OH TYR M 112 " pdb=" OE2 GLU M 124 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASP A 25 " pdb=" N THR A 26 " model vdw 2.235 3.120 nonbonded pdb=" NZ LYS E 103 " pdb=" OP2 G F 603 " model vdw 2.247 3.120 nonbonded pdb=" OD1 ASP G 25 " pdb=" N THR G 26 " model vdw 2.248 3.120 nonbonded pdb=" OH TYR G 112 " pdb=" OE2 GLU G 124 " model vdw 2.254 3.040 ... (remaining 103460 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 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (n \ ame N or name CA or name C or name O or name CB )) or resid 48 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB )) or resid 58 thro \ ugh 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 114 or (resid 115 and (name N or name C \ A or name C or name O or name CB )) or resid 116 through 118 or (resid 119 throu \ gh 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thr \ ough 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) \ or resid 125 through 129 or (resid 130 through 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 through 153 or (resid 154 and (name N o \ r name CA or name C or name O or name CB )) or resid 155 through 163 or (resid 1 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 165 through \ 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 206)) selection = (chain 'C' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 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 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 114 or (resid 115 and (name N or name CA or name C or \ name O or name CB )) or resid 116 through 119 or (resid 120 and (name N or name \ CA or name C or name O or name 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 129 o \ r (resid 130 through 138 and (name N or name CA or name C or name O or name CB ) \ ) or resid 139 through 153 or (resid 154 and (name N or name CA or name C or nam \ e O or name CB )) or resid 155 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 throu \ gh 179 or (resid 180 through 181 and (name N or name CA or name C or name O or n \ ame CB )) or resid 182 through 183 or (resid 184 and (name N or name CA or name \ C or name O or name CB )) or resid 185 through 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 206)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 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 60 or (res \ id 61 through 62 and (name N or name CA or name C or name O or name CB )) or res \ id 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 CB )) or resid 74 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 1 \ 23 or (resid 124 and (name N or name CA or name C or name O or name CB )) or res \ id 125 through 128 or (resid 129 through 138 and (name N or name CA or name C or \ name O or name CB )) or resid 139 through 153 or (resid 154 and (name N or name \ CA or name C or name O or name CB )) or resid 155 through 163 or (resid 164 and \ (name N or name CA or name C or name O or name CB )) or resid 165 through 166 o \ r (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 n \ ame 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 183 or (resid \ 184 and (name N or name CA or name C or name O or name CB )) or resid 185 throu \ gh 206)) selection = (chain 'G' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 17 or (resid 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 35 or (resid 36 and (n \ ame N or name CA or name C or name O or name CB )) or resid 37 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB )) or resid 58 thro \ ugh 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 114 or (resid 115 and (name N or name C \ A or name C or name O or name CB )) or resid 116 through 118 or (resid 119 throu \ gh 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thr \ ough 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) \ or resid 125 through 128 or (resid 129 through 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 through 153 or (resid 154 and (name N o \ r name CA or name C or name O or name CB )) or resid 155 through 166 or (resid 1 \ 67 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 n \ ame O or name CB )) or resid 175 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 183 or (res \ id 184 and (name N or name CA or name C or name O or name CB )) or resid 185 thr \ ough 198 or (resid 199 and (name N or name CA or name C or name O or name CB )) \ or resid 200 through 206)) selection = (chain 'I' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB )) or resid 37 through 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 or (resid 49 through 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 56 or (res \ id 57 and (name N or name CA or name C or name O or name CB )) or resid 58 throu \ gh 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or r \ esid 68 through 69 or (resid 70 through 73 and (name N or name CA or name C or n \ ame O or name CB )) or resid 74 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 throug \ h 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thro \ ugh 128 or (resid 129 through 138 and (name N or name CA or name C or name O or \ name CB )) or resid 139 through 166 or (resid 167 through 168 and (name N or nam \ e CA or name C or name O or name CB )) or resid 169 through 172 or (resid 173 th \ rough 174 and (name N or name CA or name C or name O or name CB )) or resid 175 \ or (resid 176 through 177 and (name N or name CA or name C or name O or name CB \ )) or resid 178 through 183 or (resid 184 and (name N or name CA or name C or na \ me O or name CB )) or resid 185 through 206)) selection = (chain 'K' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 or (resid 49 throu \ gh 50 and (name N or name CA or name C or name O or name CB )) or resid 51 throu \ gh 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or r \ esid 58 through 60 or (resid 61 through 62 and (name N or name CA or name C or n \ ame O or name CB )) or resid 63 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 throug \ h 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thro \ ugh 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) o \ r resid 125 through 128 or (resid 129 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 153 or (resid 154 and (name N or \ name CA or name C or name O or name CB )) or resid 155 through 163 or (resid 16 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 165 through \ 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 176 or (resid 177 and (n \ ame N or name CA or name C or name O or name CB )) or resid 178 through 183 or ( \ resid 184 and (name N or name CA or name C or name O or name CB )) or resid 185 \ through 206)) selection = (chain 'M' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 or (resid 49 throu \ gh 50 and (name N or name CA or name C or name O or name CB )) or resid 51 throu \ gh 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or r \ esid 58 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 69 or (resid 70 through 73 and (name N or name CA o \ r name C or name O or name CB )) or resid 74 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 (res \ id 119 through 120 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 129 or (resid 130 through 138 and (name N or na \ me CA or name C or name O or name CB )) or resid 139 through 153 or (resid 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 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 176 or (resid 177 and (name \ N or name CA or name C or name O or name CB )) or resid 178 through 183 or (res \ id 184 and (name N or name CA or name C or name O or name CB )) or resid 185 thr \ ough 206)) selection = (chain 'O' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 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 60 or (res \ id 61 through 62 and (name N or name CA or name C or name O or name CB )) or res \ id 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 CB )) or resid 74 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 or name CA or name C or name O or name CB )) or res \ id 121 through 123 or (resid 124 and (name N or name CA or name C or name O or n \ ame CB )) or resid 125 through 128 or (resid 129 through 138 and (name N or name \ CA or name C or name O or name CB )) or resid 139 through 153 or (resid 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 163 o \ r (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 65 through 166 or (resid 167 through 168 and (name N or name CA or name C or nam \ e 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 176 or (resid \ 177 and (name N or name CA or name C or name O or name CB )) or resid 178 throu \ gh 179 or (resid 180 through 181 and (name N or name CA or name C or name O or n \ ame 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 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.440 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.006 0.062 12934 Z= 0.404 Angle : 0.779 11.568 17672 Z= 0.459 Chirality : 0.053 0.214 2127 Planarity : 0.004 0.029 2203 Dihedral : 13.507 85.969 4604 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.73 (0.20), residues: 1624 helix: 0.27 (0.18), residues: 752 sheet: 0.55 (0.22), residues: 248 loop : 1.07 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 197 HIS 0.005 0.002 HIS K 7 PHE 0.021 0.002 PHE G 78 TYR 0.030 0.003 TYR E 151 ARG 0.011 0.002 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.472 Fit side-chains REVERT: C 124 GLU cc_start: 0.8326 (tt0) cc_final: 0.8057 (tt0) REVERT: G 115 ARG cc_start: 0.7548 (mmt180) cc_final: 0.7251 (mtp180) REVERT: G 173 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7158 (mm-30) REVERT: I 36 ASP cc_start: 0.8467 (m-30) cc_final: 0.8231 (m-30) REVERT: K 25 ASP cc_start: 0.7604 (t70) cc_final: 0.7385 (t70) REVERT: O 95 MET cc_start: 0.9122 (tpt) cc_final: 0.8833 (tpt) REVERT: O 124 GLU cc_start: 0.7910 (tt0) cc_final: 0.7664 (tt0) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2619 time to fit residues: 69.8269 Evaluate side-chains 163 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 67 optimal weight: 7.9990 chunk 41 optimal weight: 0.0070 chunk 81 optimal weight: 0.0370 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.4080 ------------------------------------------------------------------------------- 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 13 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 ASN M 54 GLN M 184 GLN O 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12934 Z= 0.162 Angle : 0.460 5.506 17672 Z= 0.254 Chirality : 0.044 0.127 2127 Planarity : 0.003 0.023 2203 Dihedral : 11.121 64.065 2040 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.68 % Allowed : 2.87 % Favored : 96.45 % 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: 1.78 (0.22), residues: 1624 helix: 1.50 (0.20), residues: 752 sheet: 1.11 (0.24), residues: 248 loop : 1.03 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 197 HIS 0.003 0.001 HIS M 116 PHE 0.013 0.001 PHE E 78 TYR 0.012 0.001 TYR A 151 ARG 0.003 0.000 ARG M 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 1.402 Fit side-chains REVERT: C 201 ASP cc_start: 0.7810 (t0) cc_final: 0.7575 (t0) REVERT: E 95 MET cc_start: 0.8617 (tpp) cc_final: 0.8407 (tpp) REVERT: G 27 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7360 (mm-30) REVERT: G 115 ARG cc_start: 0.7506 (mmt180) cc_final: 0.7234 (mtp180) REVERT: G 173 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6999 (mm-30) REVERT: I 191 ASN cc_start: 0.8566 (t0) cc_final: 0.7850 (m-40) REVERT: K 8 GLN cc_start: 0.8092 (mp10) cc_final: 0.7727 (mm-40) REVERT: O 25 ASP cc_start: 0.8370 (t0) cc_final: 0.8000 (t0) outliers start: 8 outliers final: 5 residues processed: 185 average time/residue: 0.2738 time to fit residues: 70.8603 Evaluate side-chains 164 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 54 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 157 optimal weight: 0.1980 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 13 ASN C 54 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 GLN I 184 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12934 Z= 0.280 Angle : 0.498 5.004 17672 Z= 0.271 Chirality : 0.046 0.135 2127 Planarity : 0.003 0.027 2203 Dihedral : 11.367 64.113 2040 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.84 % Allowed : 4.81 % Favored : 94.34 % 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 (0.21), residues: 1624 helix: 1.21 (0.19), residues: 752 sheet: 1.10 (0.25), residues: 248 loop : 0.54 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 197 HIS 0.005 0.001 HIS M 79 PHE 0.017 0.002 PHE G 78 TYR 0.014 0.002 TYR G 17 ARG 0.004 0.001 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.325 Fit side-chains REVERT: G 27 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7159 (mm-30) REVERT: G 173 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7302 (mm-30) REVERT: I 191 ASN cc_start: 0.8541 (t0) cc_final: 0.8244 (t0) REVERT: K 49 THR cc_start: 0.8336 (p) cc_final: 0.8098 (p) REVERT: M 65 LEU cc_start: 0.7582 (tp) cc_final: 0.7156 (mt) REVERT: O 25 ASP cc_start: 0.8399 (t0) cc_final: 0.8160 (t0) outliers start: 10 outliers final: 7 residues processed: 168 average time/residue: 0.2573 time to fit residues: 62.2896 Evaluate side-chains 162 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain O residue 61 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: 10.0000 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 34 HIS ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN M 184 GLN M 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12934 Z= 0.323 Angle : 0.508 4.928 17672 Z= 0.274 Chirality : 0.047 0.140 2127 Planarity : 0.004 0.029 2203 Dihedral : 11.337 64.130 2040 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.27 % Allowed : 5.49 % Favored : 93.24 % 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: 0.94 (0.21), residues: 1624 helix: 0.99 (0.19), residues: 752 sheet: 1.01 (0.26), residues: 248 loop : 0.17 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 139 HIS 0.006 0.001 HIS M 79 PHE 0.017 0.002 PHE G 78 TYR 0.016 0.002 TYR G 17 ARG 0.004 0.001 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.448 Fit side-chains REVERT: C 27 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7511 (mm-30) REVERT: E 95 MET cc_start: 0.8665 (tpp) cc_final: 0.8381 (tpp) REVERT: I 47 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6307 (m-30) outliers start: 15 outliers final: 8 residues processed: 167 average time/residue: 0.2481 time to fit residues: 60.6109 Evaluate side-chains 167 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 164 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 0.0050 chunk 131 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN M 184 GLN O 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12934 Z= 0.279 Angle : 0.476 4.744 17672 Z= 0.259 Chirality : 0.045 0.134 2127 Planarity : 0.003 0.030 2203 Dihedral : 11.207 64.103 2040 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.93 % Allowed : 6.59 % Favored : 92.48 % 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: 1624 helix: 0.99 (0.19), residues: 752 sheet: 0.81 (0.26), residues: 248 loop : -0.01 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 139 HIS 0.004 0.001 HIS C 79 PHE 0.016 0.002 PHE G 78 TYR 0.012 0.002 TYR E 151 ARG 0.003 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.419 Fit side-chains REVERT: A 206 SER cc_start: 0.6798 (p) cc_final: 0.6575 (t) REVERT: I 47 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: K 47 ASP cc_start: 0.7774 (p0) cc_final: 0.7528 (p0) REVERT: M 65 LEU cc_start: 0.7649 (tp) cc_final: 0.7355 (mt) outliers start: 11 outliers final: 9 residues processed: 170 average time/residue: 0.2415 time to fit residues: 59.8719 Evaluate side-chains 172 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.0870 chunk 139 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 HIS O 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12934 Z= 0.124 Angle : 0.387 4.725 17672 Z= 0.216 Chirality : 0.042 0.123 2127 Planarity : 0.003 0.026 2203 Dihedral : 10.855 64.002 2040 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.59 % Allowed : 7.18 % Favored : 92.23 % 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: 1.13 (0.22), residues: 1624 helix: 1.25 (0.20), residues: 760 sheet: 1.02 (0.26), residues: 248 loop : 0.14 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 139 HIS 0.003 0.000 HIS C 79 PHE 0.013 0.001 PHE G 78 TYR 0.014 0.001 TYR E 151 ARG 0.004 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 168 time to evaluate : 1.465 Fit side-chains REVERT: I 47 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6268 (m-30) outliers start: 7 outliers final: 5 residues processed: 174 average time/residue: 0.2567 time to fit residues: 63.7198 Evaluate side-chains 166 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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** A 184 GLN G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12934 Z= 0.280 Angle : 0.473 4.751 17672 Z= 0.255 Chirality : 0.045 0.134 2127 Planarity : 0.003 0.029 2203 Dihedral : 11.057 64.100 2040 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.18 % Allowed : 7.35 % Favored : 91.47 % 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: 0.91 (0.21), residues: 1624 helix: 1.14 (0.20), residues: 752 sheet: 0.81 (0.27), residues: 248 loop : -0.02 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 139 HIS 0.004 0.001 HIS C 79 PHE 0.018 0.002 PHE G 78 TYR 0.014 0.002 TYR G 17 ARG 0.004 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.519 Fit side-chains REVERT: A 206 SER cc_start: 0.6814 (p) cc_final: 0.6566 (t) REVERT: I 47 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6298 (m-30) outliers start: 14 outliers final: 9 residues processed: 168 average time/residue: 0.2439 time to fit residues: 59.8272 Evaluate side-chains 168 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 0.0070 chunk 121 optimal weight: 5.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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** A 184 GLN G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 HIS O 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12934 Z= 0.136 Angle : 0.391 4.736 17672 Z= 0.217 Chirality : 0.042 0.124 2127 Planarity : 0.003 0.026 2203 Dihedral : 10.825 63.997 2040 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.76 % Allowed : 7.85 % Favored : 91.39 % 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: 1.12 (0.22), residues: 1624 helix: 1.27 (0.20), residues: 760 sheet: 1.02 (0.27), residues: 248 loop : 0.10 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 139 HIS 0.003 0.000 HIS C 79 PHE 0.014 0.001 PHE G 78 TYR 0.008 0.001 TYR G 17 ARG 0.004 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.371 Fit side-chains REVERT: C 27 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7392 (mm-30) REVERT: I 47 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6228 (m-30) REVERT: K 49 THR cc_start: 0.8531 (p) cc_final: 0.8210 (p) REVERT: O 13 ASN cc_start: 0.8145 (p0) cc_final: 0.7867 (p0) outliers start: 9 outliers final: 6 residues processed: 174 average time/residue: 0.2516 time to fit residues: 62.9520 Evaluate side-chains 171 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER 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: 6.9990 chunk 134 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 overall best weight: 6.0588 ------------------------------------------------------------------------------- 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** A 184 GLN G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN M 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 12934 Z= 0.528 Angle : 0.616 6.433 17672 Z= 0.324 Chirality : 0.051 0.184 2127 Planarity : 0.005 0.034 2203 Dihedral : 11.364 64.261 2040 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.35 % Allowed : 7.43 % Favored : 91.22 % 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: 0.54 (0.21), residues: 1624 helix: 0.88 (0.19), residues: 736 sheet: 0.67 (0.27), residues: 256 loop : -0.27 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I 139 HIS 0.007 0.002 HIS C 79 PHE 0.021 0.002 PHE G 78 TYR 0.020 0.003 TYR G 17 ARG 0.007 0.001 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.462 Fit side-chains REVERT: A 206 SER cc_start: 0.6785 (p) cc_final: 0.6574 (t) REVERT: E 95 MET cc_start: 0.8548 (tpp) cc_final: 0.8221 (tpp) REVERT: I 47 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6194 (m-30) REVERT: I 51 ASP cc_start: 0.8608 (m-30) cc_final: 0.8346 (m-30) outliers start: 16 outliers final: 10 residues processed: 171 average time/residue: 0.2421 time to fit residues: 60.4861 Evaluate side-chains 170 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 115 ARG Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 72 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12934 Z= 0.138 Angle : 0.397 4.700 17672 Z= 0.221 Chirality : 0.042 0.124 2127 Planarity : 0.003 0.028 2203 Dihedral : 10.879 64.002 2040 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.68 % Allowed : 8.19 % Favored : 91.13 % 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: 0.84 (0.21), residues: 1624 helix: 1.12 (0.20), residues: 760 sheet: 0.77 (0.27), residues: 248 loop : -0.11 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 139 HIS 0.002 0.000 HIS K 160 PHE 0.015 0.001 PHE G 78 TYR 0.011 0.001 TYR G 17 ARG 0.004 0.000 ARG A 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 1.453 Fit side-chains REVERT: A 206 SER cc_start: 0.6708 (p) cc_final: 0.6457 (t) REVERT: G 151 TYR cc_start: 0.7486 (t80) cc_final: 0.7035 (t80) REVERT: I 47 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6218 (m-30) REVERT: O 13 ASN cc_start: 0.8288 (p0) cc_final: 0.8022 (p0) REVERT: O 27 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7308 (mm-30) REVERT: O 188 MET cc_start: 0.7645 (tpp) cc_final: 0.7387 (mmt) outliers start: 8 outliers final: 6 residues processed: 179 average time/residue: 0.2489 time to fit residues: 63.8859 Evaluate side-chains 175 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 168 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** A 184 GLN G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN M 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.106746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.095371 restraints weight = 15503.035| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.00 r_work: 0.2774 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12934 Z= 0.423 Angle : 0.550 5.238 17672 Z= 0.293 Chirality : 0.049 0.157 2127 Planarity : 0.004 0.035 2203 Dihedral : 11.217 64.197 2040 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.93 % Allowed : 8.36 % Favored : 90.71 % 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: 0.43 (0.21), residues: 1624 helix: 0.86 (0.19), residues: 752 sheet: 0.52 (0.27), residues: 248 loop : -0.40 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP I 139 HIS 0.006 0.001 HIS C 79 PHE 0.019 0.002 PHE G 78 TYR 0.016 0.002 TYR E 17 ARG 0.005 0.001 ARG C 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.79 seconds wall clock time: 46 minutes 29.84 seconds (2789.84 seconds total)