Starting phenix.real_space_refine on Tue Mar 19 02:37:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/03_2024/7mqe_23944.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/03_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_23944/03_2024/7mqe_23944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/03_2024/7mqe_23944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/03_2024/7mqe_23944.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqe_23944/03_2024/7mqe_23944.pdb" } 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 Residue "A GLU 124": "OE1" <-> "OE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 167": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.75, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 4.39 Conformation dependent library (CDL) restraints added in 2.3 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: 1.17 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: 3.06 Time building geometry restraints manager: 4.78 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: 98.31 - 105.46: 222 105.46 - 112.60: 6748 112.60 - 119.75: 4117 119.75 - 126.90: 5697 126.90 - 134.04: 204 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 2.520 nonbonded pdb=" OH TYR C 112 " pdb=" OE2 GLU C 124 " model vdw 2.327 2.440 nonbonded pdb=" OG1 THR K 26 " pdb=" OD1 ASP K 84 " model vdw 2.428 2.440 nonbonded pdb=" OG1 THR G 26 " pdb=" OD1 ASP G 84 " model vdw 2.435 2.440 nonbonded pdb=" O LYS I 103 " pdb=" OG SER I 106 " model vdw 2.442 2.440 ... (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 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 1.310 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.670 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.710 ------------------------------------------------------------------------------- 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 : 1.389 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: 0.2297 time to fit residues: 64.9747 Evaluate side-chains 161 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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: 10.0000 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 145 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12424 Z= 0.147 Angle : 0.452 7.338 16988 Z= 0.242 Chirality : 0.043 0.130 2064 Planarity : 0.003 0.022 2095 Dihedral : 11.338 85.072 2030 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.77 % Allowed : 4.44 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.22), residues: 1607 helix: 1.86 (0.20), residues: 730 sheet: 0.98 (0.24), residues: 253 loop : 0.95 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 197 HIS 0.002 0.000 HIS G 160 PHE 0.015 0.001 PHE C 78 TYR 0.009 0.001 TYR G 151 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: 8 poor density : 174 time to evaluate : 1.271 Fit side-chains REVERT: A 154 SER cc_start: 0.8500 (p) cc_final: 0.8016 (m) REVERT: C 188 MET cc_start: 0.7626 (tpp) cc_final: 0.7158 (tpp) REVERT: E 25 ASP cc_start: 0.7713 (t0) cc_final: 0.7427 (t0) REVERT: E 201 ASP cc_start: 0.7229 (t0) cc_final: 0.6827 (t0) REVERT: G 27 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7644 (mm-30) REVERT: G 157 LEU cc_start: 0.8110 (mt) cc_final: 0.7791 (mt) REVERT: I 25 ASP cc_start: 0.7852 (t70) cc_final: 0.7486 (t0) REVERT: I 95 MET cc_start: 0.8111 (tpp) cc_final: 0.7807 (tpp) REVERT: I 120 GLU cc_start: 0.8453 (tp30) cc_final: 0.8243 (tp30) REVERT: K 157 LEU cc_start: 0.8245 (mt) cc_final: 0.8017 (mt) REVERT: K 164 ASP cc_start: 0.7167 (m-30) cc_final: 0.6699 (m-30) REVERT: M 188 MET cc_start: 0.7992 (tpp) cc_final: 0.7726 (mmm) REVERT: O 71 ASP cc_start: 0.6767 (t0) cc_final: 0.6486 (t0) REVERT: O 188 MET cc_start: 0.7531 (mmm) cc_final: 0.6695 (tpp) outliers start: 8 outliers final: 2 residues processed: 176 average time/residue: 0.2187 time to fit residues: 57.2147 Evaluate side-chains 149 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 THR 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: 0.8980 chunk 120 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 42 GLN C 8 GLN C 54 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12424 Z= 0.199 Angle : 0.443 7.675 16988 Z= 0.236 Chirality : 0.044 0.131 2064 Planarity : 0.003 0.023 2095 Dihedral : 10.801 63.872 2018 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.45 % Allowed : 5.98 % Favored : 92.57 % 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: 1.85 (0.22), residues: 1607 helix: 1.77 (0.20), residues: 730 sheet: 1.26 (0.27), residues: 257 loop : 0.70 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 197 HIS 0.004 0.001 HIS E 90 PHE 0.015 0.001 PHE C 78 TYR 0.010 0.001 TYR C 151 ARG 0.003 0.000 ARG I 172 *********************** 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 170 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.323 Fit side-chains REVERT: A 124 GLU cc_start: 0.8086 (tt0) cc_final: 0.7510 (tt0) REVERT: A 201 ASP cc_start: 0.8094 (t0) cc_final: 0.7453 (t0) REVERT: C 188 MET cc_start: 0.7722 (tpp) cc_final: 0.7192 (tpp) REVERT: E 25 ASP cc_start: 0.7786 (t0) cc_final: 0.7501 (t0) REVERT: E 201 ASP cc_start: 0.6979 (t0) cc_final: 0.6537 (t0) REVERT: G 157 LEU cc_start: 0.8105 (mt) cc_final: 0.7837 (mt) REVERT: I 25 ASP cc_start: 0.7941 (t70) cc_final: 0.7631 (t70) REVERT: I 95 MET cc_start: 0.8340 (tpp) cc_final: 0.7832 (tpp) REVERT: K 64 ASN cc_start: 0.8537 (m-40) cc_final: 0.8310 (m-40) REVERT: M 124 GLU cc_start: 0.7853 (tt0) cc_final: 0.7117 (tt0) REVERT: M 201 ASP cc_start: 0.7900 (t0) cc_final: 0.7307 (t0) REVERT: O 71 ASP cc_start: 0.7003 (t0) cc_final: 0.6576 (t0) REVERT: O 188 MET cc_start: 0.7545 (mmm) cc_final: 0.6882 (tpp) outliers start: 15 outliers final: 13 residues processed: 163 average time/residue: 0.2153 time to fit residues: 52.5731 Evaluate side-chains 160 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN 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 G residue 155 ASP Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 194 LEU 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: 9.9990 chunk 109 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 205 HIS ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN O 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2131 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= 0.266 Angle : 0.459 8.188 16988 Z= 0.244 Chirality : 0.044 0.126 2064 Planarity : 0.003 0.024 2095 Dihedral : 10.911 63.791 2018 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.64 % Allowed : 6.46 % 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: 1.61 (0.22), residues: 1607 helix: 1.50 (0.20), residues: 731 sheet: 1.35 (0.28), residues: 257 loop : 0.59 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 197 HIS 0.009 0.001 HIS C 7 PHE 0.015 0.001 PHE C 78 TYR 0.012 0.001 TYR A 151 ARG 0.002 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 164 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.415 Fit side-chains REVERT: A 201 ASP cc_start: 0.8027 (t0) cc_final: 0.7437 (t0) REVERT: C 188 MET cc_start: 0.7772 (tpp) cc_final: 0.7309 (tpp) REVERT: E 25 ASP cc_start: 0.7693 (t0) cc_final: 0.7397 (t0) REVERT: G 157 LEU cc_start: 0.8165 (mt) cc_final: 0.7891 (mt) REVERT: I 95 MET cc_start: 0.8355 (tpp) cc_final: 0.7753 (tpp) REVERT: K 64 ASN cc_start: 0.8531 (m-40) cc_final: 0.8309 (m-40) REVERT: M 124 GLU cc_start: 0.7937 (tt0) cc_final: 0.7201 (tt0) REVERT: M 201 ASP cc_start: 0.7865 (t0) cc_final: 0.7331 (t0) REVERT: O 8 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8250 (mp10) REVERT: O 71 ASP cc_start: 0.6995 (t0) cc_final: 0.6473 (t0) REVERT: O 188 MET cc_start: 0.7527 (mmm) cc_final: 0.6876 (tpp) outliers start: 17 outliers final: 16 residues processed: 153 average time/residue: 0.2016 time to fit residues: 47.1495 Evaluate side-chains 157 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 E residue 16 ASN Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 39 CYS Chi-restraints excluded: chain K residue 198 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN C 54 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12424 Z= 0.119 Angle : 0.385 8.344 16988 Z= 0.206 Chirality : 0.042 0.124 2064 Planarity : 0.003 0.023 2095 Dihedral : 10.660 63.750 2018 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.06 % Allowed : 7.62 % Favored : 91.32 % 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: 1.96 (0.22), residues: 1607 helix: 2.03 (0.20), residues: 702 sheet: 1.70 (0.28), residues: 257 loop : 0.40 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP K 139 HIS 0.002 0.000 HIS I 90 PHE 0.012 0.001 PHE O 78 TYR 0.017 0.001 TYR K 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 168 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.496 Fit side-chains REVERT: A 122 CYS cc_start: 0.7859 (m) cc_final: 0.7616 (m) REVERT: A 124 GLU cc_start: 0.7843 (tt0) cc_final: 0.7585 (tt0) REVERT: A 201 ASP cc_start: 0.8048 (t0) cc_final: 0.7369 (t0) REVERT: A 206 SER cc_start: 0.6365 (p) cc_final: 0.5990 (t) REVERT: C 71 ASP cc_start: 0.7090 (t0) cc_final: 0.6847 (t0) REVERT: C 188 MET cc_start: 0.7794 (tpp) cc_final: 0.7315 (tpp) REVERT: E 25 ASP cc_start: 0.7564 (t0) cc_final: 0.7212 (t0) REVERT: E 201 ASP cc_start: 0.6976 (t0) cc_final: 0.6595 (t0) REVERT: G 27 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6866 (mm-30) REVERT: G 157 LEU cc_start: 0.7992 (mt) cc_final: 0.7691 (mt) REVERT: G 194 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7988 (tp) REVERT: I 25 ASP cc_start: 0.7740 (t70) cc_final: 0.7409 (t0) REVERT: I 95 MET cc_start: 0.8333 (tpp) cc_final: 0.7866 (tpp) REVERT: M 17 TYR cc_start: 0.7654 (m-80) cc_final: 0.7358 (m-80) REVERT: M 201 ASP cc_start: 0.7923 (t0) cc_final: 0.7279 (t0) REVERT: O 8 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8120 (mp10) REVERT: O 71 ASP cc_start: 0.6919 (t0) cc_final: 0.6642 (t0) REVERT: O 188 MET cc_start: 0.7503 (mmm) cc_final: 0.6961 (tpp) REVERT: O 191 ASN cc_start: 0.8630 (t0) cc_final: 0.8393 (t0) outliers start: 11 outliers final: 8 residues processed: 163 average time/residue: 0.2061 time to fit residues: 51.6598 Evaluate side-chains 156 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 E residue 16 ASN Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 122 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 GLN C 54 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 HIS ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12424 Z= 0.214 Angle : 0.426 8.561 16988 Z= 0.226 Chirality : 0.043 0.126 2064 Planarity : 0.003 0.026 2095 Dihedral : 10.657 63.780 2018 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.12 % Allowed : 7.14 % Favored : 90.74 % 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: 1.72 (0.22), residues: 1607 helix: 1.58 (0.20), residues: 732 sheet: 1.69 (0.29), residues: 257 loop : 0.49 (0.28), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 139 HIS 0.003 0.001 HIS M 79 PHE 0.013 0.001 PHE C 78 TYR 0.011 0.001 TYR C 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 161 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.309 Fit side-chains REVERT: A 201 ASP cc_start: 0.8015 (t0) cc_final: 0.7445 (t0) REVERT: A 206 SER cc_start: 0.6427 (p) cc_final: 0.6036 (t) REVERT: C 188 MET cc_start: 0.7951 (tpp) cc_final: 0.7544 (tpp) REVERT: E 25 ASP cc_start: 0.7677 (t0) cc_final: 0.7332 (t0) REVERT: E 95 MET cc_start: 0.7829 (mmm) cc_final: 0.7588 (tpt) REVERT: G 157 LEU cc_start: 0.8057 (mt) cc_final: 0.7752 (mt) REVERT: I 95 MET cc_start: 0.8341 (tpp) cc_final: 0.7729 (tpp) REVERT: M 17 TYR cc_start: 0.7665 (m-80) cc_final: 0.7363 (m-80) REVERT: M 124 GLU cc_start: 0.7993 (tt0) cc_final: 0.7700 (tm-30) REVERT: M 201 ASP cc_start: 0.7876 (t0) cc_final: 0.7361 (t0) REVERT: O 8 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8088 (mp10) REVERT: O 188 MET cc_start: 0.7562 (mmm) cc_final: 0.7039 (tpp) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.2003 time to fit residues: 46.8633 Evaluate side-chains 150 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 122 CYS Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain K residue 198 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 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: 4.9990 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2505 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= 0.369 Angle : 0.511 8.621 16988 Z= 0.269 Chirality : 0.046 0.131 2064 Planarity : 0.004 0.028 2095 Dihedral : 10.933 63.822 2018 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.83 % Allowed : 8.58 % Favored : 89.59 % 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: 1.27 (0.22), residues: 1607 helix: 1.25 (0.20), residues: 732 sheet: 1.34 (0.29), residues: 254 loop : 0.28 (0.28), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 197 HIS 0.010 0.001 HIS C 7 PHE 0.014 0.002 PHE C 78 TYR 0.020 0.002 TYR K 151 ARG 0.004 0.001 ARG C 5 *********************** 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 156 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.463 Fit side-chains REVERT: A 201 ASP cc_start: 0.8093 (t0) cc_final: 0.7859 (t0) REVERT: C 188 MET cc_start: 0.8060 (tpp) cc_final: 0.7430 (tpp) REVERT: E 25 ASP cc_start: 0.7717 (t0) cc_final: 0.7386 (t0) REVERT: E 95 MET cc_start: 0.8329 (mmm) cc_final: 0.7894 (mmm) REVERT: G 157 LEU cc_start: 0.8182 (mt) cc_final: 0.7925 (mt) REVERT: I 95 MET cc_start: 0.8495 (tpp) cc_final: 0.8039 (tpp) REVERT: O 8 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8017 (mp10) REVERT: O 188 MET cc_start: 0.7553 (mmm) cc_final: 0.6933 (tpp) outliers start: 19 outliers final: 15 residues processed: 147 average time/residue: 0.2048 time to fit residues: 46.2524 Evaluate side-chains 148 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 122 CYS 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 G residue 198 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 198 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 0.3980 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12424 Z= 0.138 Angle : 0.401 8.713 16988 Z= 0.215 Chirality : 0.042 0.233 2064 Planarity : 0.003 0.026 2095 Dihedral : 10.640 63.776 2018 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.87 % Allowed : 9.26 % 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: 1.61 (0.22), residues: 1607 helix: 1.58 (0.20), residues: 732 sheet: 1.60 (0.29), residues: 257 loop : 0.32 (0.28), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 139 HIS 0.002 0.000 HIS C 90 PHE 0.013 0.001 PHE O 78 TYR 0.020 0.001 TYR K 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 148 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.272 Fit side-chains REVERT: A 124 GLU cc_start: 0.7960 (tt0) cc_final: 0.7533 (tm-30) REVERT: A 135 GLN cc_start: 0.5795 (tt0) cc_final: 0.5276 (pt0) REVERT: A 201 ASP cc_start: 0.8187 (t0) cc_final: 0.7425 (t0) REVERT: C 188 MET cc_start: 0.8058 (tpp) cc_final: 0.7684 (tpp) REVERT: E 25 ASP cc_start: 0.7609 (t0) cc_final: 0.7292 (t0) REVERT: E 201 ASP cc_start: 0.6986 (t0) cc_final: 0.6686 (t0) REVERT: G 157 LEU cc_start: 0.8067 (mt) cc_final: 0.7806 (mt) REVERT: M 17 TYR cc_start: 0.7837 (m-80) cc_final: 0.7548 (m-80) REVERT: M 124 GLU cc_start: 0.7785 (tt0) cc_final: 0.7555 (tm-30) REVERT: M 201 ASP cc_start: 0.8138 (t0) cc_final: 0.7436 (t0) REVERT: O 8 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8018 (mp10) REVERT: O 148 GLN cc_start: 0.8131 (mt0) cc_final: 0.7903 (mt0) REVERT: O 188 MET cc_start: 0.7521 (mmm) cc_final: 0.6999 (tpp) REVERT: O 191 ASN cc_start: 0.8602 (t0) cc_final: 0.8386 (t0) outliers start: 9 outliers final: 8 residues processed: 142 average time/residue: 0.2109 time to fit residues: 45.8905 Evaluate side-chains 144 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 155 ASP Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain I residue 16 ASN 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: 0.7980 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN O 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12424 Z= 0.384 Angle : 0.516 8.823 16988 Z= 0.272 Chirality : 0.047 0.222 2064 Planarity : 0.003 0.027 2095 Dihedral : 11.000 63.835 2018 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.45 % Allowed : 9.16 % 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: 1.24 (0.20), residues: 730 sheet: 1.25 (0.29), residues: 254 loop : 0.11 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 197 HIS 0.005 0.001 HIS A 116 PHE 0.015 0.002 PHE C 78 TYR 0.022 0.002 TYR K 151 ARG 0.004 0.001 ARG E 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 157 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.347 Fit side-chains REVERT: A 135 GLN cc_start: 0.5961 (tt0) cc_final: 0.4792 (pp30) REVERT: A 201 ASP cc_start: 0.8099 (t0) cc_final: 0.7851 (t0) REVERT: C 188 MET cc_start: 0.8069 (tpp) cc_final: 0.7441 (tpp) REVERT: E 25 ASP cc_start: 0.7709 (t0) cc_final: 0.7409 (t0) REVERT: I 95 MET cc_start: 0.8502 (tpp) cc_final: 0.8057 (tpp) REVERT: O 8 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8027 (mp10) REVERT: O 154 SER cc_start: 0.8840 (p) cc_final: 0.8532 (t) REVERT: O 188 MET cc_start: 0.7648 (mmm) cc_final: 0.6967 (tpp) outliers start: 15 outliers final: 12 residues processed: 147 average time/residue: 0.2017 time to fit residues: 45.6006 Evaluate side-chains 152 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 122 CYS 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 16 ASN Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain O residue 61 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: 3.9990 chunk 92 optimal weight: 0.0570 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 126 optimal weight: 0.0980 chunk 13 optimal weight: 0.0010 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.2308 ------------------------------------------------------------------------------- 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 54 GLN ** E 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12424 Z= 0.154 Angle : 0.413 9.167 16988 Z= 0.220 Chirality : 0.043 0.176 2064 Planarity : 0.003 0.026 2095 Dihedral : 10.720 63.779 2018 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.68 % Allowed : 10.41 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1607 helix: 1.50 (0.20), residues: 731 sheet: 1.47 (0.30), residues: 257 loop : 0.22 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 139 HIS 0.002 0.000 HIS K 79 PHE 0.013 0.001 PHE O 78 TYR 0.023 0.001 TYR A 151 ARG 0.002 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 147 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.324 Fit side-chains REVERT: A 124 GLU cc_start: 0.7987 (tt0) cc_final: 0.7542 (tm-30) REVERT: A 135 GLN cc_start: 0.5944 (tt0) cc_final: 0.5227 (pt0) REVERT: A 201 ASP cc_start: 0.8188 (t0) cc_final: 0.7877 (t0) REVERT: C 188 MET cc_start: 0.8068 (tpp) cc_final: 0.7651 (tpp) REVERT: E 201 ASP cc_start: 0.7007 (t0) cc_final: 0.6612 (t0) REVERT: I 95 MET cc_start: 0.8490 (tpp) cc_final: 0.8115 (tpt) REVERT: M 17 TYR cc_start: 0.7880 (m-80) cc_final: 0.7560 (m-80) REVERT: M 124 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7539 (tm-30) REVERT: O 8 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8062 (mp10) REVERT: O 148 GLN cc_start: 0.8159 (mt0) cc_final: 0.7882 (mt0) REVERT: O 154 SER cc_start: 0.8819 (p) cc_final: 0.8446 (t) REVERT: O 188 MET cc_start: 0.7592 (mmm) cc_final: 0.7082 (tpp) REVERT: O 191 ASN cc_start: 0.8665 (t0) cc_final: 0.8424 (t0) outliers start: 7 outliers final: 7 residues processed: 143 average time/residue: 0.2008 time to fit residues: 44.1229 Evaluate side-chains 145 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 G residue 167 GLU Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain I residue 16 ASN 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: 10.0000 chunk 38 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3197 r_free = 0.3197 target = 0.111731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.097518 restraints weight = 16581.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098990 restraints weight = 12788.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.100344 restraints weight = 10528.728| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2704 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= 0.206 Angle : 0.430 9.152 16988 Z= 0.228 Chirality : 0.043 0.166 2064 Planarity : 0.003 0.025 2095 Dihedral : 10.755 63.801 2018 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.87 % Allowed : 10.13 % 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: 1.45 (0.22), residues: 1607 helix: 1.49 (0.20), residues: 731 sheet: 1.57 (0.30), residues: 254 loop : 0.17 (0.28), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 139 HIS 0.003 0.001 HIS A 79 PHE 0.013 0.001 PHE O 78 TYR 0.020 0.002 TYR K 151 ARG 0.002 0.000 ARG I 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.79 seconds wall clock time: 36 minutes 3.26 seconds (2163.26 seconds total)