Starting phenix.real_space_refine on Sun Sep 13 03:49:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqe_23944/09_2026/7mqe_23944.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqe_23944/09_2026/7mqe_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7mqe_23944/09_2026/7mqe_23944.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqe_23944/09_2026/7mqe_23944.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mqe_23944/09_2026/7mqe_23944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqe_23944/09_2026/7mqe_23944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqe_23944/09_2026/7mqe_23944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqe_23944/09_2026/7mqe_23944.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10872 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 48 5.16 5 C 7752 2.51 5 N 2257 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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, 'ASP:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 2} 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: {'GLU:plan': 8, 'ASP:plan': 13, 'ASN:plan1': 4, 'ARG:plan': 3, 'GLN:plan1': 2} 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, 'ASP:plan': 11, 'ASN:plan1': 4} 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: {'GLU:plan': 9, 'ASP:plan': 13, 'ASN:plan1': 3, 'ARG:plan': 3, 'GLN:plan1': 2} 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, 'ASP:plan': 13, 'ASN:plan1': 3} 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, 'ASP:plan': 12, 'ASN:plan1': 3, 'ARG:plan': 3} 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: {'ASP:plan': 13, 'ASN:plan1': 3, 'ARG:plan': 2, 'GLU:plan': 9, 'GLN:plan1': 3} 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: {'GLU:plan': 9, 'ASP:plan': 13, 'ASN:plan1': 5, 'ARG:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 2.87, per 1000 atoms: 0.24 Number of scatterers: 12163 At special positions: 0 Unit cell: (107.88, 117.8, 105.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 16 15.00 O 2090 8.00 N 2257 7.00 C 7752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 530.6 milliseconds 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: 0.35 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: 2.01 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3987 1.34 - 1.46: 2396 1.46 - 1.58: 5953 1.58 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 12424 Sorted by residual: bond pdb=" C ARG C 67 " pdb=" N LEU C 68 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.36e-02 5.41e+03 1.18e+01 bond pdb=" N VAL O 41 " pdb=" CA VAL O 41 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.20e-02 6.94e+03 8.71e+00 bond pdb=" N VAL G 128 " pdb=" CA VAL G 128 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.30e+00 bond pdb=" N VAL C 40 " pdb=" CA VAL C 40 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.14e+00 bond pdb=" N VAL C 41 " pdb=" CA VAL C 41 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.08e+00 ... (remaining 12419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15813 1.55 - 3.11: 997 3.11 - 4.66: 151 4.66 - 6.21: 23 6.21 - 7.76: 4 Bond angle restraints: 16988 Sorted by residual: angle pdb=" N GLN A 135 " pdb=" CA GLN A 135 " pdb=" C GLN A 135 " ideal model delta sigma weight residual 112.54 107.67 4.87 1.22e+00 6.72e-01 1.59e+01 angle pdb=" CA VAL G 128 " pdb=" C VAL G 128 " pdb=" O VAL G 128 " ideal model delta sigma weight residual 121.59 117.83 3.76 1.03e+00 9.43e-01 1.33e+01 angle pdb=" CA LEU C 43 " pdb=" C LEU C 43 " pdb=" O LEU C 43 " ideal model delta sigma weight residual 121.68 117.50 4.18 1.18e+00 7.18e-01 1.25e+01 angle pdb=" N GLN G 135 " pdb=" CA GLN G 135 " pdb=" C GLN G 135 " ideal model delta sigma weight residual 112.89 108.53 4.36 1.24e+00 6.50e-01 1.23e+01 angle pdb=" CA LEU O 43 " pdb=" C LEU O 43 " pdb=" O LEU O 43 " ideal model delta sigma weight residual 121.46 117.55 3.91 1.17e+00 7.31e-01 1.12e+01 ... (remaining 16983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 6868 18.08 - 36.16: 315 36.16 - 54.24: 67 54.24 - 72.33: 17 72.33 - 90.41: 19 Dihedral angle restraints: 7286 sinusoidal: 2538 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 7283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1558 0.066 - 0.133: 433 0.133 - 0.199: 50 0.199 - 0.265: 14 0.265 - 0.331: 9 Chirality restraints: 2064 Sorted by residual: chirality pdb=" P G P 603 " pdb=" OP1 G P 603 " pdb=" OP2 G P 603 " pdb=" O5' G P 603 " both_signs ideal model delta sigma weight residual True 2.17 2.50 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" P G H 603 " pdb=" OP1 G H 603 " pdb=" OP2 G H 603 " pdb=" O5' G H 603 " both_signs ideal model delta sigma weight residual True 2.17 2.50 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" P G F 603 " pdb=" OP1 G F 603 " pdb=" OP2 G F 603 " pdb=" O5' G F 603 " both_signs ideal model delta sigma weight residual True 2.17 2.50 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2061 not shown) Planarity restraints: 2095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA M 153 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ALA M 153 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA M 153 " -0.013 2.00e-02 2.50e+03 pdb=" N SER M 154 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 37 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C ARG C 37 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG C 37 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU C 38 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG O 37 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ARG O 37 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG O 37 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU O 38 " 0.011 2.00e-02 2.50e+03 ... (remaining 2092 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3527 2.83 - 3.34: 10699 3.34 - 3.86: 19724 3.86 - 4.38: 22813 4.38 - 4.90: 40034 Nonbonded interactions: 96797 Sorted by model distance: nonbonded pdb=" NH1 ARG I 82 " pdb=" OD2 ASP I 193 " model vdw 2.308 3.120 nonbonded pdb=" OH TYR C 112 " pdb=" OE2 GLU C 124 " model vdw 2.327 3.040 nonbonded pdb=" OG1 THR K 26 " pdb=" OD1 ASP K 84 " model vdw 2.428 3.040 nonbonded pdb=" OG1 THR G 26 " pdb=" OD1 ASP G 84 " model vdw 2.435 3.040 nonbonded pdb=" O LYS I 103 " pdb=" OG SER I 106 " model vdw 2.442 3.040 ... (remaining 96792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 46 or (resid 47 and (name N or nam \ e CA or name C or name O or name CB )) or resid 48 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 105 or (resid 106 and (name N or name CA or name C or name O o \ r name CB )) or resid 107 through 114 or (resid 115 and (name N or name CA or na \ me C or name O or name CB )) or resid 116 through 118 or (resid 119 through 120 \ and (name N or name CA or name C or name O or name CB )) or resid 121 through 12 \ 3 or (resid 124 and (name N or name CA or name C or name O or name CB )) or resi \ d 125 through 126 or (resid 127 through 131 and (name N or name CA or name C or \ name O or name CB )) or resid 136 through 148 or (resid 149 through 150 and (nam \ e N or name CA or name C or name O or name CB )) or resid 151 through 163 or (re \ sid 164 through 165 and (name N or name CA or name C or name O or name CB )) or \ resid 166 through 176 or (resid 177 and (name N or name CA or name C or name O o \ r name CB )) or resid 178 through 200 or (resid 201 and (name N or name CA or na \ me C or name O or name CB )) or resid 202 through 206)) selection = (chain 'C' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 66 or (resid 67 and (name N or name \ CA or name C or name O or name CB )) or resid 68 through 70 or (resid 71 through \ 73 and (name N or name CA or name C or name O or name CB )) or resid 74 through \ 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or res \ id 95 through 119 or (resid 120 and (name N or name CA or name C or name O or na \ me CB )) or resid 121 through 123 or (resid 124 and (name N or name CA or name C \ or name O or name CB )) or resid 125 through 131 or resid 136 through 148 or (r \ esid 149 through 150 and (name N or name CA or name C or name O or name CB )) or \ resid 151 through 164 or (resid 165 and (name N or name CA or name C or name O \ or name CB )) or resid 166 or (resid 167 through 168 and (name N or name CA or n \ ame C or name O or name CB )) or resid 169 through 176 or (resid 177 and (name N \ or name CA or name C or name O or name CB )) or resid 178 through 179 or (resid \ 180 through 181 and (name N or name CA or name C or name O or name CB )) or res \ id 182 through 206)) selection = (chain 'E' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 or (resid 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 60 or (r \ esid 61 through 62 and (name N or name CA or name C or name O or name CB )) or r \ esid 63 through 66 or (resid 67 and (name N or name CA or name C or name O or na \ me CB )) or resid 68 through 105 or (resid 106 and (name N or name CA or name C \ or name O or name CB )) or resid 107 through 154 or (resid 155 and (name N or na \ me CA or name C or name O or name CB )) or resid 156 through 163 or (resid 164 t \ hrough 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ through 172 or (resid 173 through 174 and (name N or name CA or name C or name \ O or name CB )) or resid 175 through 176 or (resid 177 and (name N or name CA or \ name C or name O or name CB )) or resid 178 through 179 or (resid 180 through 1 \ 81 and (name N or name CA or name C or name O or name CB )) or resid 182 through \ 200 or (resid 201 and (name N or name CA or name C or name O or name CB )) or r \ esid 202 through 206)) selection = (chain 'G' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 63 or (resid 64 and (na \ me N or name CA or name C or name O or name CB )) or resid 65 through 105 or (re \ sid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 th \ rough 114 or (resid 115 and (name N or name CA or name C or name O or name CB )) \ or resid 116 through 127 or (resid 128 through 131 and (name N or name CA or na \ me C or name O or name CB )) or resid 136 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 4 or (resid 155 and (name N or name CA or name C or name O or name CB )) or resi \ d 156 through 164 or (resid 165 and (name N or name CA or name C or name O or na \ me CB )) or resid 166 or (resid 167 through 168 and (name N or name CA or name C \ or name O or name CB )) or resid 169 through 172 or (resid 173 through 174 and \ (name N or name CA or name C or name O or name CB )) or resid 175 through 206)) selection = (chain 'I' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 27 or (resid 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 66 or (res \ id 67 and (name N or name CA or name C or name O or name CB )) or resid 68 throu \ gh 69 or (resid 70 through 73 and (name N or name CA or name C or name O or name \ CB )) or resid 74 through 93 or (resid 94 and (name N or name CA or name C or n \ ame O or name CB )) or resid 95 through 105 or (resid 106 and (name N or name CA \ or name C or name O or name CB )) or resid 107 through 119 or (resid 120 and (n \ ame N or name CA or name C or name O or name CB )) or resid 121 through 128 or ( \ resid 129 through 138 and (name N or name CA or name C or name O or name CB )) o \ r resid 139 through 154 or (resid 155 and (name N or name CA or name C or name O \ or name CB )) or resid 156 through 176 or (resid 177 and (name N or name CA or \ name C or name O or name CB )) or resid 178 through 179 or (resid 180 through 18 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 182 through \ 206)) selection = (chain 'K' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 56 or (resid 57 and (name N or nam \ e CA or name C or name O or name CB )) or resid 58 through 60 or (resid 61 throu \ gh 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 105 or (resid 106 and (name N or name CA or name C or name O or name CB )) \ or resid 107 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 118 or (resid 119 through 120 and (name N o \ r name CA or name C or name O or name CB )) or resid 121 through 127 or (resid 1 \ 28 through 131 and (name N or name CA or name C or name O or name CB )) or (resi \ d 136 through 138 and (name N or name CA or name C or name O or name CB )) or re \ sid 139 through 148 or (resid 149 through 150 and (name N or name CA or name C o \ r name O or name CB )) or resid 151 through 163 or (resid 164 through 165 and (n \ ame N or name CA or name C or name O or name CB )) or resid 166 through 172 or ( \ resid 173 through 174 and (name N or name CA or name C or name O or name CB )) o \ r resid 175 through 176 or (resid 177 and (name N or name CA or name C or name O \ or name CB )) or resid 178 through 206)) selection = (chain 'M' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 or (resid 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 69 or (resid 70 through 73 and (name N or name CA or name C or \ name O or name CB )) or resid 74 through 93 or (resid 94 and (name N or name CA \ or name C or name O or name CB )) or resid 95 through 105 or (resid 106 and (na \ me N or name CA or name C or name O or name CB )) or resid 107 through 114 or (r \ esid 115 and (name N or name CA or name C or name O or name CB )) or resid 116 t \ hrough 123 or (resid 124 and (name N or name CA or name C or name O or name CB ) \ ) or resid 125 through 127 or (resid 128 through 131 and (name N or name CA or n \ ame C or name O or name CB )) or resid 136 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 1 \ 64 or (resid 165 and (name N or name CA or name C or name O or name CB )) or res \ id 166 through 176 or (resid 177 and (name N or name CA or name C or name O or n \ ame CB )) or resid 178 through 179 or (resid 180 through 181 and (name N or name \ CA or name C or name O or name CB )) or resid 182 through 200 or (resid 201 and \ (name N or name CA or name C or name O or name CB )) or resid 202 through 206)) \ selection = (chain 'O' and ((resid 2 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB )) or resid 58 through 60 or (resid 61 through 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 66 or (resid \ 67 and (name N or name CA or name C or name O or name CB )) or resid 68 through \ 69 or (resid 70 through 73 and (name N or name CA or name C or name O or name C \ B )) or resid 74 through 105 or (resid 106 and (name N or name CA or name C or n \ ame O or name CB )) or resid 107 through 118 or (resid 119 through 120 and (name \ N or name CA or name C or name O or name CB )) or resid 121 through 123 or (res \ id 124 and (name N or name CA or name C or name O or name CB )) or resid 125 thr \ ough 131 or resid 136 through 148 or (resid 149 through 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 164 or (resid 165 and \ (name N or name CA or name C or name O or name CB )) or resid 166 or (resid 167 \ through 168 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 9 through 176 or (resid 177 and (name N or name CA or name C or name O or name C \ B )) or resid 178 through 179 or (resid 180 through 181 and (name N or name CA o \ r name C or name O or name CB )) or resid 182 through 206)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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= 0.374 Angle : 0.851 7.763 16988 Z= 0.509 Chirality : 0.064 0.331 2064 Planarity : 0.005 0.032 2095 Dihedral : 13.242 90.408 4188 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.002 ARG A 37 TYR 0.026 0.003 TYR E 17 PHE 0.021 0.003 PHE M 78 TRP 0.026 0.003 TRP C 197 HIS 0.007 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.37 (12424) covalent geometry : angle 0.85148 / 0.51 (16988) hydrogen bonds : bond 0.11922 / 8.14 ( 589) hydrogen bonds : angle 7.46675 / 5.28 ( 1767) *********************** 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 to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 0.482 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: 0.1070 time to fit residues: 31.0821 Evaluate side-chains 161 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN M 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103280 restraints weight = 16397.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.104409 restraints weight = 13222.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.105486 restraints weight = 11309.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106102 restraints weight = 9944.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106320 restraints weight = 9042.038| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 12424 Z= 0.093 Angle : 0.456 7.349 16988 Z= 0.243 Chirality : 0.044 0.129 2064 Planarity : 0.003 0.022 2095 Dihedral : 6.324 88.712 1934 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.39 % Allowed : 4.63 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.22), residues: 1607 helix: 1.81 (0.20), residues: 729 sheet: 0.90 (0.24), residues: 253 loop : 1.05 (0.28), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.009 0.001 TYR A 151 PHE 0.015 0.001 PHE C 78 TRP 0.005 0.001 TRP E 197 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (12424) covalent geometry : angle 0.45583 / 0.24 (16988) hydrogen bonds : bond 0.03433 / 2.36 ( 589) hydrogen bonds : angle 5.55094 / 3.97 ( 1767) *********************** 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 181 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 177 time to evaluate : 0.503 Fit side-chains REVERT: C 25 ASP cc_start: 0.7896 (t70) cc_final: 0.7688 (t0) REVERT: C 188 MET cc_start: 0.7615 (tpp) cc_final: 0.7241 (tpp) REVERT: E 25 ASP cc_start: 0.7774 (t0) cc_final: 0.7565 (t0) REVERT: G 27 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7499 (mm-30) REVERT: G 157 LEU cc_start: 0.7983 (mt) cc_final: 0.7681 (mt) REVERT: I 95 MET cc_start: 0.8009 (tpp) cc_final: 0.7760 (tpp) REVERT: K 164 ASP cc_start: 0.6939 (m-30) cc_final: 0.6547 (m-30) REVERT: O 188 MET cc_start: 0.7481 (mmm) cc_final: 0.6922 (tpp) outliers start: 4 outliers final: 0 residues processed: 179 average time/residue: 0.1035 time to fit residues: 27.8501 Evaluate side-chains 147 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 92 optimal weight: 0.0570 chunk 117 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 32 GLN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN C 54 GLN C 205 HIS ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN I 42 GLN M 8 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.108625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.094325 restraints weight = 16846.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.095988 restraints weight = 12876.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.097027 restraints weight = 10546.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.097953 restraints weight = 9087.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098739 restraints weight = 8105.549| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1991 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= 0.244 Angle : 0.560 7.619 16988 Z= 0.294 Chirality : 0.048 0.134 2064 Planarity : 0.004 0.042 2095 Dihedral : 4.922 26.198 1922 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.45 % Allowed : 6.27 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.21), residues: 1607 helix: 1.34 (0.20), residues: 729 sheet: 0.92 (0.27), residues: 254 loop : 0.67 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 82 TYR 0.011 0.002 TYR M 17 PHE 0.017 0.002 PHE C 78 TRP 0.009 0.002 TRP E 197 HIS 0.005 0.001 HIS M 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.24 (12424) covalent geometry : angle 0.56046 / 0.29 (16988) hydrogen bonds : bond 0.04332 / 2.97 ( 589) hydrogen bonds : angle 5.63506 / 4.03 ( 1767) *********************** 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 164 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.498 Fit side-chains REVERT: A 124 GLU cc_start: 0.7943 (tt0) cc_final: 0.7454 (tt0) REVERT: C 25 ASP cc_start: 0.8031 (t70) cc_final: 0.7749 (t0) REVERT: C 27 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7762 (mm-30) REVERT: C 188 MET cc_start: 0.7773 (tpp) cc_final: 0.7283 (tpp) REVERT: E 95 MET cc_start: 0.8368 (tpp) cc_final: 0.8160 (tpt) REVERT: I 95 MET cc_start: 0.8317 (tpp) cc_final: 0.7774 (tpp) REVERT: M 124 GLU cc_start: 0.7853 (tt0) cc_final: 0.7290 (tt0) REVERT: O 8 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8339 (mp10) REVERT: O 188 MET cc_start: 0.7647 (mmm) cc_final: 0.7141 (tpp) outliers start: 15 outliers final: 13 residues processed: 155 average time/residue: 0.0997 time to fit residues: 23.7693 Evaluate side-chains 161 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain I residue 39 CYS 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 128 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 8 GLN C 54 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.095496 restraints weight = 16603.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.097207 restraints weight = 12672.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.098392 restraints weight = 10238.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.099375 restraints weight = 8777.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.099787 restraints weight = 7774.418| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12424 Z= 0.176 Angle : 0.480 8.279 16988 Z= 0.255 Chirality : 0.046 0.128 2064 Planarity : 0.003 0.030 2095 Dihedral : 4.717 26.715 1922 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.54 % Allowed : 7.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.22), residues: 1607 helix: 1.31 (0.20), residues: 730 sheet: 0.85 (0.27), residues: 257 loop : 0.51 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 82 TYR 0.019 0.002 TYR K 151 PHE 0.016 0.001 PHE O 78 TRP 0.006 0.001 TRP E 197 HIS 0.003 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (12424) covalent geometry : angle 0.48047 / 0.25 (16988) hydrogen bonds : bond 0.03802 / 2.60 ( 589) hydrogen bonds : angle 5.35827 / 3.83 ( 1767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3214 Ramachandran restraints generated. 1607 Oldfield, 0 Emsley, 1607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.422 Fit side-chains REVERT: C 188 MET cc_start: 0.7802 (tpp) cc_final: 0.7391 (tpp) REVERT: E 25 ASP cc_start: 0.8148 (t0) cc_final: 0.7918 (t70) REVERT: E 95 MET cc_start: 0.8411 (tpp) cc_final: 0.8047 (tpp) REVERT: I 95 MET cc_start: 0.8342 (tpp) cc_final: 0.7719 (tpp) REVERT: M 17 TYR cc_start: 0.7942 (m-80) cc_final: 0.7736 (m-80) REVERT: O 8 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8248 (mp10) REVERT: O 67 ARG cc_start: 0.7294 (mtm180) cc_final: 0.7091 (ttp-110) REVERT: O 188 MET cc_start: 0.7576 (mmm) cc_final: 0.7095 (tpp) outliers start: 16 outliers final: 15 residues processed: 158 average time/residue: 0.0944 time to fit residues: 23.0879 Evaluate side-chains 156 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain 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 K residue 61 SER Chi-restraints excluded: chain M residue 16 ASN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 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 116 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.095433 restraints weight = 16790.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.097076 restraints weight = 12839.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.098351 restraints weight = 10489.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.099363 restraints weight = 8923.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.099978 restraints weight = 7826.072| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12424 Z= 0.169 Angle : 0.470 8.347 16988 Z= 0.249 Chirality : 0.045 0.126 2064 Planarity : 0.003 0.029 2095 Dihedral : 4.655 29.897 1922 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.54 % Allowed : 7.81 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.22), residues: 1607 helix: 1.25 (0.20), residues: 732 sheet: 0.87 (0.28), residues: 257 loop : 0.43 (0.28), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 172 TYR 0.012 0.002 TYR A 151 PHE 0.015 0.001 PHE C 78 TRP 0.005 0.001 TRP I 197 HIS 0.006 0.001 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (12424) covalent geometry : angle 0.46984 / 0.25 (16988) hydrogen bonds : bond 0.03761 / 2.57 ( 589) hydrogen bonds : angle 5.28430 / 3.77 ( 1767) *********************** 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 160 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.373 Fit side-chains REVERT: C 188 MET cc_start: 0.7965 (tpp) cc_final: 0.7610 (tpp) REVERT: E 95 MET cc_start: 0.8357 (tpp) cc_final: 0.8038 (tpp) REVERT: I 25 ASP cc_start: 0.8191 (t0) cc_final: 0.7785 (t70) REVERT: I 95 MET cc_start: 0.8330 (tpp) cc_final: 0.7698 (tpp) REVERT: O 8 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8216 (mp10) REVERT: O 67 ARG cc_start: 0.7300 (mtm180) cc_final: 0.7098 (ttp-110) REVERT: O 188 MET cc_start: 0.7556 (mmm) cc_final: 0.7141 (tpp) outliers start: 16 outliers final: 16 residues processed: 151 average time/residue: 0.0931 time to fit residues: 21.9327 Evaluate side-chains 154 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 K residue 61 SER Chi-restraints excluded: chain M residue 16 ASN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 122 CYS Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 86 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN C 54 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.094405 restraints weight = 16654.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.096084 restraints weight = 12710.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.097340 restraints weight = 10313.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.098121 restraints weight = 8834.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098895 restraints weight = 7887.784| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12424 Z= 0.211 Angle : 0.501 8.467 16988 Z= 0.264 Chirality : 0.046 0.131 2064 Planarity : 0.003 0.029 2095 Dihedral : 4.773 33.693 1922 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.83 % Allowed : 7.81 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.22), residues: 1607 helix: 1.11 (0.20), residues: 731 sheet: 0.75 (0.28), residues: 257 loop : 0.29 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 146 TYR 0.016 0.002 TYR A 151 PHE 0.016 0.001 PHE C 78 TRP 0.005 0.001 TRP O 197 HIS 0.006 0.001 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (12424) covalent geometry : angle 0.50091 / 0.26 (16988) hydrogen bonds : bond 0.04009 / 2.75 ( 589) hydrogen bonds : angle 5.33562 / 3.80 ( 1767) *********************** 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 162 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.470 Fit side-chains REVERT: A 135 GLN cc_start: 0.5978 (tt0) cc_final: 0.5258 (pt0) REVERT: C 188 MET cc_start: 0.8032 (tpp) cc_final: 0.7537 (tpp) REVERT: I 95 MET cc_start: 0.8343 (tpp) cc_final: 0.7860 (tpp) REVERT: O 8 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8175 (mp10) REVERT: O 188 MET cc_start: 0.7647 (mmm) cc_final: 0.7199 (tpp) outliers start: 19 outliers final: 16 residues processed: 153 average time/residue: 0.0839 time to fit residues: 20.2243 Evaluate side-chains 153 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 I residue 39 CYS Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 70 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 8 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.097366 restraints weight = 16429.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.099085 restraints weight = 12492.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100376 restraints weight = 10086.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.101154 restraints weight = 8619.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101903 restraints weight = 7676.066| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12424 Z= 0.105 Angle : 0.421 8.842 16988 Z= 0.224 Chirality : 0.043 0.123 2064 Planarity : 0.003 0.027 2095 Dihedral : 4.388 29.204 1922 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.87 % Allowed : 8.78 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1607 helix: 1.39 (0.20), residues: 731 sheet: 0.98 (0.28), residues: 257 loop : 0.36 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 172 TYR 0.017 0.001 TYR A 151 PHE 0.013 0.001 PHE O 78 TRP 0.005 0.001 TRP K 139 HIS 0.006 0.001 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (12424) covalent geometry : angle 0.42101 / 0.22 (16988) hydrogen bonds : bond 0.03257 / 2.24 ( 589) hydrogen bonds : angle 5.06077 / 3.59 ( 1767) *********************** 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 159 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.522 Fit side-chains REVERT: A 42 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: A 135 GLN cc_start: 0.5987 (tt0) cc_final: 0.5348 (pt0) REVERT: C 188 MET cc_start: 0.8058 (tpp) cc_final: 0.7688 (tpp) REVERT: E 25 ASP cc_start: 0.8156 (t0) cc_final: 0.7859 (t70) REVERT: E 95 MET cc_start: 0.8285 (tpp) cc_final: 0.7781 (tpp) REVERT: I 95 MET cc_start: 0.8373 (tpp) cc_final: 0.7915 (tpp) REVERT: K 27 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7004 (mm-30) REVERT: K 129 ASN cc_start: 0.7450 (t0) cc_final: 0.7117 (t0) REVERT: O 8 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8143 (mp10) REVERT: O 106 SER cc_start: 0.9348 (t) cc_final: 0.9137 (t) REVERT: O 188 MET cc_start: 0.7659 (mmm) cc_final: 0.7223 (tpp) outliers start: 9 outliers final: 8 residues processed: 155 average time/residue: 0.0939 time to fit residues: 22.5873 Evaluate side-chains 150 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 122 CYS Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain O residue 122 CYS Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 81 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN C 54 GLN E 32 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.095251 restraints weight = 16734.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.097002 restraints weight = 12678.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098262 restraints weight = 10279.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098825 restraints weight = 8714.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099773 restraints weight = 7891.559| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12424 Z= 0.180 Angle : 0.479 9.119 16988 Z= 0.252 Chirality : 0.045 0.129 2064 Planarity : 0.003 0.028 2095 Dihedral : 4.560 31.616 1922 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.25 % Allowed : 9.26 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.22), residues: 1607 helix: 1.23 (0.20), residues: 731 sheet: 0.85 (0.29), residues: 257 loop : 0.21 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 172 TYR 0.017 0.002 TYR A 151 PHE 0.015 0.001 PHE C 78 TRP 0.005 0.001 TRP M 139 HIS 0.003 0.001 HIS M 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (12424) covalent geometry : angle 0.47915 / 0.25 (16988) hydrogen bonds : bond 0.03744 / 2.57 ( 589) hydrogen bonds : angle 5.18625 / 3.67 ( 1767) *********************** 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 156 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.470 Fit side-chains REVERT: A 135 GLN cc_start: 0.6040 (tt0) cc_final: 0.5265 (pt0) REVERT: C 188 MET cc_start: 0.8042 (tpp) cc_final: 0.7722 (tpp) REVERT: E 25 ASP cc_start: 0.8234 (t0) cc_final: 0.7913 (t70) REVERT: E 95 MET cc_start: 0.8396 (tpp) cc_final: 0.7985 (tpp) REVERT: I 95 MET cc_start: 0.8414 (tpp) cc_final: 0.7973 (tpp) REVERT: O 8 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8136 (mp10) REVERT: O 188 MET cc_start: 0.7638 (mmm) cc_final: 0.7256 (tpp) outliers start: 13 outliers final: 13 residues processed: 148 average time/residue: 0.0837 time to fit residues: 19.5718 Evaluate side-chains 153 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 124 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain M residue 16 ASN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 122 CYS Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 145 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 101 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.096730 restraints weight = 16550.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.098452 restraints weight = 12515.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099747 restraints weight = 10155.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.100322 restraints weight = 8624.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.101023 restraints weight = 7796.706| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2673 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= 0.125 Angle : 0.438 9.154 16988 Z= 0.231 Chirality : 0.044 0.127 2064 Planarity : 0.003 0.027 2095 Dihedral : 4.403 30.198 1922 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.54 % Allowed : 9.16 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.22), residues: 1607 helix: 1.35 (0.20), residues: 731 sheet: 0.94 (0.29), residues: 257 loop : 0.21 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 172 TYR 0.020 0.001 TYR A 151 PHE 0.013 0.001 PHE O 78 TRP 0.004 0.001 TRP K 139 HIS 0.002 0.001 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (12424) covalent geometry : angle 0.43790 / 0.23 (16988) hydrogen bonds : bond 0.03396 / 2.33 ( 589) hydrogen bonds : angle 5.08008 / 3.59 ( 1767) *********************** 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 162 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.515 Fit side-chains REVERT: A 135 GLN cc_start: 0.6053 (tt0) cc_final: 0.5327 (pt0) REVERT: A 201 ASP cc_start: 0.8259 (t0) cc_final: 0.7955 (t0) REVERT: C 188 MET cc_start: 0.8059 (tpp) cc_final: 0.7739 (tpp) REVERT: E 25 ASP cc_start: 0.8202 (t0) cc_final: 0.7873 (t70) REVERT: I 95 MET cc_start: 0.8386 (tpp) cc_final: 0.7960 (tpp) REVERT: K 27 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7037 (mm-30) REVERT: O 8 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8127 (mp10) REVERT: O 106 SER cc_start: 0.9379 (t) cc_final: 0.9166 (t) REVERT: O 188 MET cc_start: 0.7760 (mmm) cc_final: 0.7370 (tpp) outliers start: 16 outliers final: 15 residues processed: 153 average time/residue: 0.0829 time to fit residues: 19.9755 Evaluate side-chains 157 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 122 CYS 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 K residue 61 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain M residue 16 ASN Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 122 CYS Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.096372 restraints weight = 16709.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.097918 restraints weight = 12725.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.099321 restraints weight = 10393.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.100124 restraints weight = 8877.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.100957 restraints weight = 7894.634| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12424 Z= 0.141 Angle : 0.449 9.429 16988 Z= 0.237 Chirality : 0.044 0.129 2064 Planarity : 0.003 0.027 2095 Dihedral : 4.402 30.227 1922 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.64 % Allowed : 9.16 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1607 helix: 1.34 (0.20), residues: 731 sheet: 0.94 (0.29), residues: 257 loop : 0.19 (0.28), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 172 TYR 0.021 0.001 TYR A 151 PHE 0.014 0.001 PHE C 78 TRP 0.004 0.001 TRP M 139 HIS 0.003 0.001 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (12424) covalent geometry : angle 0.44876 / 0.24 (16988) hydrogen bonds : bond 0.03478 / 2.39 ( 589) hydrogen bonds : angle 5.09355 / 3.60 ( 1767) ********************** 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 159 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.402 Fit side-chains REVERT: A 135 GLN cc_start: 0.5895 (tt0) cc_final: 0.5138 (pp30) REVERT: A 201 ASP cc_start: 0.8265 (t0) cc_final: 0.7945 (t0) REVERT: C 188 MET cc_start: 0.8058 (tpp) cc_final: 0.7747 (tpp) REVERT: E 25 ASP cc_start: 0.8061 (t0) cc_final: 0.7813 (t70) REVERT: I 95 MET cc_start: 0.8380 (tpp) cc_final: 0.7960 (tpp) REVERT: K 27 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7059 (mm-30) REVERT: O 8 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8135 (mp10) REVERT: O 106 SER cc_start: 0.9398 (t) cc_final: 0.9189 (t) REVERT: O 188 MET cc_start: 0.7677 (mmm) cc_final: 0.7360 (tpp) outliers start: 17 outliers final: 17 residues processed: 148 average time/residue: 0.0907 time to fit residues: 20.9837 Evaluate side-chains 157 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 K residue 61 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain M residue 16 ASN Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 122 CYS Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 129 optimal weight: 0.0970 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.094255 restraints weight = 16852.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095873 restraints weight = 12854.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.097149 restraints weight = 10470.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.097953 restraints weight = 8955.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098724 restraints weight = 7960.498| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12424 Z= 0.222 Angle : 0.514 9.255 16988 Z= 0.269 Chirality : 0.047 0.134 2064 Planarity : 0.003 0.028 2095 Dihedral : 4.703 33.615 1922 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.64 % Allowed : 9.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.22), residues: 1607 helix: 1.14 (0.20), residues: 730 sheet: 0.70 (0.29), residues: 257 loop : 0.06 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 5 TYR 0.020 0.002 TYR A 151 PHE 0.015 0.001 PHE C 78 TRP 0.006 0.001 TRP M 139 HIS 0.006 0.001 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (12424) covalent geometry : angle 0.51439 / 0.27 (16988) hydrogen bonds : bond 0.04054 / 2.78 ( 589) hydrogen bonds : angle 5.29471 / 3.75 ( 1767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.10 seconds wall clock time: 29 minutes 56.87 seconds (1796.87 seconds total)