Starting phenix.real_space_refine on Sat Mar 7 03:25:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scb_25032/03_2026/7scb_25032.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scb_25032/03_2026/7scb_25032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7scb_25032/03_2026/7scb_25032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scb_25032/03_2026/7scb_25032.map" model { file = "/net/cci-nas-00/data/ceres_data/7scb_25032/03_2026/7scb_25032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scb_25032/03_2026/7scb_25032.cif" } resolution = 2.5 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= 0.003 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 194 5.16 5 C 23522 2.51 5 N 6298 2.21 5 O 7215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37229 Number of models: 1 Model: "" Number of chains: 54 Chain: "AA" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AB" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AC" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AD" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AE" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1254 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain: "AF" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AH" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AI" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AJ" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AK" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1322 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "AL" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AN" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AO" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AP" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AQ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AR" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AS" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AU" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AV" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AW" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AX" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AY" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AZ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BB" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "BC" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "BE" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5124 Classifications: {'peptide': 647} Link IDs: {'PTRANS': 37, 'TRANS': 609} Chain breaks: 1 Chain: "BG" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 451 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain: "BH" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1269 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain: "BI" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 277 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Chain: "AA" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AI" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AK" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AO" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AQ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AS" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AU" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AW" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AY" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'45D': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.05, per 1000 atoms: 0.24 Number of scatterers: 37229 At special positions: 0 Unit cell: (159.6, 144.9, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 194 16.00 O 7215 8.00 N 6298 7.00 C 23522 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.4 seconds 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8734 Finding SS restraints... Secondary structure from input PDB file: 256 helices and 6 sheets defined 79.7% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'AA' and resid 2 through 14 removed outlier: 3.650A pdb=" N GLUAA 14 " --> pdb=" O ASNAA 10 " (cutoff:3.500A) Processing helix chain 'AA' and resid 19 through 32 Processing helix chain 'AA' and resid 32 through 46 Processing helix chain 'AA' and resid 46 through 62 removed outlier: 3.652A pdb=" N VALAA 51 " --> pdb=" O ARGAA 47 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALAAA 54 " --> pdb=" O ILEAA 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHEAA 59 " --> pdb=" O GLYAA 55 " (cutoff:3.500A) Processing helix chain 'AA' and resid 74 through 99 removed outlier: 3.518A pdb=" N ALAAA 79 " --> pdb=" O GLUAA 75 " (cutoff:3.500A) Processing helix chain 'AA' and resid 101 through 109 Processing helix chain 'AA' and resid 111 through 120 Processing helix chain 'AA' and resid 122 through 141 removed outlier: 3.587A pdb=" N GLUAA 135 " --> pdb=" O ARGAA 131 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLYAA 139 " --> pdb=" O GLUAA 135 " (cutoff:3.500A) Processing helix chain 'AA' and resid 142 through 160 removed outlier: 3.957A pdb=" N ALAAA 151 " --> pdb=" O ALAAA 147 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYRAA 152 " --> pdb=" O GLUAA 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VALAA 156 " --> pdb=" O TYRAA 152 " (cutoff:3.500A) Processing helix chain 'AB' and resid 3 through 16 removed outlier: 3.723A pdb=" N VALAB 8 " --> pdb=" O ALAAB 4 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLNAB 15 " --> pdb=" O SERAB 11 " (cutoff:3.500A) Processing helix chain 'AB' and resid 20 through 33 removed outlier: 3.612A pdb=" N ASPAB 25 " --> pdb=" O GLYAB 21 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYSAB 26 " --> pdb=" O ALAAB 22 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEUAB 27 " --> pdb=" O ALAAB 23 " (cutoff:3.500A) Processing helix chain 'AB' and resid 33 through 47 Processing helix chain 'AB' and resid 47 through 60 removed outlier: 4.032A pdb=" N VALAB 52 " --> pdb=" O ALAAB 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALAAB 57 " --> pdb=" O LYSAB 53 " (cutoff:3.500A) Processing helix chain 'AB' and resid 74 through 99 removed outlier: 3.975A pdb=" N ALAAB 92 " --> pdb=" O TYRAB 88 " (cutoff:3.500A) Processing helix chain 'AB' and resid 102 through 107 Processing helix chain 'AB' and resid 111 through 120 removed outlier: 3.605A pdb=" N GLYAB 120 " --> pdb=" O TYRAB 116 " (cutoff:3.500A) Processing helix chain 'AB' and resid 122 through 142 removed outlier: 3.501A pdb=" N SERAB 139 " --> pdb=" O GLUAB 135 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEUAB 140 " --> pdb=" O VALAB 136 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VALAB 141 " --> pdb=" O THRAB 137 " (cutoff:3.500A) Processing helix chain 'AB' and resid 142 through 161 removed outlier: 3.880A pdb=" N TYRAB 152 " --> pdb=" O GLUAB 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 3 through 15 removed outlier: 3.646A pdb=" N ILEAC 8 " --> pdb=" O VALAC 4 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASNAC 10 " --> pdb=" O LYSAC 6 " (cutoff:3.500A) Processing helix chain 'AC' and resid 19 through 32 removed outlier: 3.657A pdb=" N ARGAC 25 " --> pdb=" O GLYAC 21 " (cutoff:3.500A) Processing helix chain 'AC' and resid 32 through 46 removed outlier: 3.719A pdb=" N ARGAC 36 " --> pdb=" O GLYAC 32 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILEAC 39 " --> pdb=" O ALAAC 35 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALAAC 40 " --> pdb=" O ARGAC 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THRAC 42 " --> pdb=" O ARGAC 38 " (cutoff:3.500A) Processing helix chain 'AC' and resid 46 through 62 removed outlier: 3.811A pdb=" N VALAC 51 " --> pdb=" O ARGAC 47 " (cutoff:3.500A) Processing helix chain 'AC' and resid 62 through 67 removed outlier: 4.550A pdb=" N VALAC 66 " --> pdb=" O ARGAC 62 " (cutoff:3.500A) Processing helix chain 'AC' and resid 75 through 99 removed outlier: 3.748A pdb=" N THRAC 80 " --> pdb=" O GLUAC 76 " (cutoff:3.500A) Processing helix chain 'AC' and resid 101 through 109 removed outlier: 3.697A pdb=" N GLUAC 105 " --> pdb=" O VALAC 101 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEUAC 109 " --> pdb=" O GLUAC 105 " (cutoff:3.500A) Processing helix chain 'AC' and resid 112 through 118 removed outlier: 3.553A pdb=" N SERAC 118 " --> pdb=" O GLUAC 114 " (cutoff:3.500A) Processing helix chain 'AC' and resid 122 through 141 removed outlier: 3.636A pdb=" N VALAC 126 " --> pdb=" O PROAC 122 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALAC 130 " --> pdb=" O VALAC 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N METAC 141 " --> pdb=" O ALAAC 137 " (cutoff:3.500A) Processing helix chain 'AC' and resid 142 through 160 removed outlier: 4.166A pdb=" N GLUAC 148 " --> pdb=" O ASPAC 144 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALAAC 149 " --> pdb=" O ASPAC 145 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALAAC 151 " --> pdb=" O ALAAC 147 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYRAC 152 " --> pdb=" O GLUAC 148 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHEAC 155 " --> pdb=" O ALAAC 151 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VALAC 156 " --> pdb=" O TYRAC 152 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N METAC 160 " --> pdb=" O VALAC 156 " (cutoff:3.500A) Processing helix chain 'AD' and resid 3 through 14 removed outlier: 3.514A pdb=" N ALAAD 7 " --> pdb=" O ASPAD 3 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VALAD 8 " --> pdb=" O ALAAD 4 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALAAD 12 " --> pdb=" O VALAD 8 " (cutoff:3.500A) Processing helix chain 'AD' and resid 20 through 33 removed outlier: 4.154A pdb=" N LYSAD 26 " --> pdb=" O ALAAD 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SERAD 29 " --> pdb=" O ASPAD 25 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYRAD 30 " --> pdb=" O LYSAD 26 " (cutoff:3.500A) Processing helix chain 'AD' and resid 33 through 47 Processing helix chain 'AD' and resid 47 through 58 removed outlier: 3.670A pdb=" N ILEAD 51 " --> pdb=" O ASNAD 47 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VALAD 52 " --> pdb=" O ALAAD 48 " (cutoff:3.500A) Processing helix chain 'AD' and resid 74 through 99 Processing helix chain 'AD' and resid 101 through 108 removed outlier: 3.928A pdb=" N ASPAD 105 " --> pdb=" O ALAAD 101 " (cutoff:3.500A) Processing helix chain 'AD' and resid 113 through 120 Processing helix chain 'AD' and resid 122 through 142 removed outlier: 3.707A pdb=" N LYSAD 134 " --> pdb=" O ILEAD 130 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLUAD 135 " --> pdb=" O GLNAD 131 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VALAD 136 " --> pdb=" O ALAAD 132 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SERAD 139 " --> pdb=" O GLUAD 135 " (cutoff:3.500A) Processing helix chain 'AD' and resid 142 through 161 removed outlier: 3.716A pdb=" N GLUAD 148 " --> pdb=" O ASPAD 144 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VALAD 151 " --> pdb=" O LYSAD 147 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYRAD 152 " --> pdb=" O GLUAD 148 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLYAD 159 " --> pdb=" O TYRAD 155 " (cutoff:3.500A) Processing helix chain 'AE' and resid 3 through 14 removed outlier: 3.589A pdb=" N GLNAE 14 " --> pdb=" O GLNAE 10 " (cutoff:3.500A) Processing helix chain 'AE' and resid 19 through 32 removed outlier: 3.648A pdb=" N PHEAE 29 " --> pdb=" O GLYAE 25 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THRAE 31 " --> pdb=" O GLNAE 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THRAE 32 " --> pdb=" O ALAAE 28 " (cutoff:3.500A) Processing helix chain 'AE' and resid 32 through 45 removed outlier: 3.706A pdb=" N ARGAE 38 " --> pdb=" O ALAAE 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALAAE 40 " --> pdb=" O ARGAE 36 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLUAE 41 " --> pdb=" O ILEAE 37 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THRAE 42 " --> pdb=" O ARGAE 38 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEUAE 43 " --> pdb=" O ILEAE 39 " (cutoff:3.500A) Processing helix chain 'AE' and resid 46 through 62 removed outlier: 3.598A pdb=" N LYSAE 60 " --> pdb=" O LYSAE 56 " (cutoff:3.500A) Processing helix chain 'AE' and resid 74 through 99 removed outlier: 3.679A pdb=" N GLNAE 80 " --> pdb=" O ARGAE 76 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEUAE 82 " --> pdb=" O TYRAE 78 " (cutoff:3.500A) Processing helix chain 'AE' and resid 101 through 109 removed outlier: 3.769A pdb=" N THRAE 107 " --> pdb=" O PROAE 103 " (cutoff:3.500A) Processing helix chain 'AE' and resid 112 through 118 removed outlier: 3.732A pdb=" N TYRAE 116 " --> pdb=" O VALAE 112 " (cutoff:3.500A) Processing helix chain 'AE' and resid 122 through 141 removed outlier: 4.116A pdb=" N ASPAE 128 " --> pdb=" O PROAE 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALAAE 129 " --> pdb=" O GLYAE 125 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THRAE 131 " --> pdb=" O VALAE 127 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VALAE 132 " --> pdb=" O ASPAE 128 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEUAE 140 " --> pdb=" O ALAAE 136 " (cutoff:3.500A) Processing helix chain 'AE' and resid 142 through 161 removed outlier: 3.749A pdb=" N ASNAE 147 " --> pdb=" O ALAAE 143 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLUAE 148 " --> pdb=" O GLUAE 144 " (cutoff:3.500A) Proline residue: AE 151 - end of helix removed outlier: 3.698A pdb=" N ILEAE 156 " --> pdb=" O TYRAE 152 " (cutoff:3.500A) Processing helix chain 'AF' and resid 3 through 16 removed outlier: 3.877A pdb=" N VALAF 8 " --> pdb=" O ALAAF 4 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILEAF 9 " --> pdb=" O ILEAF 5 " (cutoff:3.500A) Processing helix chain 'AF' and resid 20 through 33 removed outlier: 5.293A pdb=" N LYSAF 26 " --> pdb=" O ALAAF 22 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEUAF 27 " --> pdb=" O ALAAF 23 " (cutoff:3.500A) Processing helix chain 'AF' and resid 33 through 47 removed outlier: 3.557A pdb=" N ARGAF 39 " --> pdb=" O GLUAF 35 " (cutoff:3.500A) Processing helix chain 'AF' and resid 47 through 60 removed outlier: 3.975A pdb=" N VALAF 52 " --> pdb=" O ALAAF 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYSAF 53 " --> pdb=" O ALAAF 49 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYSAF 58 " --> pdb=" O GLUAF 54 " (cutoff:3.500A) Processing helix chain 'AF' and resid 74 through 99 Processing helix chain 'AF' and resid 102 through 107 Processing helix chain 'AF' and resid 111 through 120 removed outlier: 3.728A pdb=" N ASNAF 117 " --> pdb=" O LYSAF 113 " (cutoff:3.500A) Processing helix chain 'AF' and resid 122 through 141 Processing helix chain 'AF' and resid 142 through 161 removed outlier: 3.611A pdb=" N LYSAF 147 " --> pdb=" O ALAAF 143 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLUAF 148 " --> pdb=" O ASPAF 144 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VALAF 151 " --> pdb=" O LYSAF 147 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYRAF 152 " --> pdb=" O GLUAF 148 " (cutoff:3.500A) Processing helix chain 'AH' and resid 3 through 14 Processing helix chain 'AH' and resid 19 through 32 removed outlier: 4.289A pdb=" N ARGAH 25 " --> pdb=" O GLYAH 21 " (cutoff:3.500A) Processing helix chain 'AH' and resid 33 through 46 removed outlier: 3.598A pdb=" N SERAH 46 " --> pdb=" O THRAH 42 " (cutoff:3.500A) Processing helix chain 'AH' and resid 46 through 62 removed outlier: 3.673A pdb=" N VALAH 51 " --> pdb=" O ARGAH 47 " (cutoff:3.500A) Processing helix chain 'AH' and resid 63 through 66 Processing helix chain 'AH' and resid 75 through 99 removed outlier: 3.585A pdb=" N ALAAH 79 " --> pdb=" O GLUAH 75 " (cutoff:3.500A) Processing helix chain 'AH' and resid 101 through 109 removed outlier: 3.569A pdb=" N ILEAH 107 " --> pdb=" O PROAH 103 " (cutoff:3.500A) Processing helix chain 'AH' and resid 111 through 120 Processing helix chain 'AH' and resid 122 through 140 removed outlier: 3.595A pdb=" N VALAH 126 " --> pdb=" O PROAH 122 " (cutoff:3.500A) Processing helix chain 'AH' and resid 142 through 161 removed outlier: 3.921A pdb=" N TYRAH 152 " --> pdb=" O GLUAH 148 " (cutoff:3.500A) Processing helix chain 'AI' and resid 3 through 14 removed outlier: 3.601A pdb=" N VALAI 8 " --> pdb=" O ALAAI 4 " (cutoff:3.500A) Processing helix chain 'AI' and resid 20 through 47 removed outlier: 3.837A pdb=" N LYSAI 26 " --> pdb=" O ALAAI 22 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEUAI 27 " --> pdb=" O ALAAI 23 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLUAI 35 " --> pdb=" O PHEAI 31 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEUAI 36 " --> pdb=" O ALAAI 32 " (cutoff:3.500A) Processing helix chain 'AI' and resid 47 through 60 removed outlier: 3.868A pdb=" N VALAI 52 " --> pdb=" O ALAAI 48 " (cutoff:3.500A) Processing helix chain 'AI' and resid 74 through 99 Processing helix chain 'AI' and resid 103 through 108 Processing helix chain 'AI' and resid 112 through 120 Processing helix chain 'AI' and resid 122 through 141 removed outlier: 3.765A pdb=" N GLNAI 128 " --> pdb=" O SERAI 124 " (cutoff:3.500A) Processing helix chain 'AI' and resid 142 through 161 removed outlier: 3.755A pdb=" N GLUAI 148 " --> pdb=" O ASPAI 144 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYRAI 152 " --> pdb=" O GLUAI 148 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 3 through 15 removed outlier: 3.802A pdb=" N GLUAJ 14 " --> pdb=" O ASNAJ 10 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 19 through 32 Processing helix chain 'AJ' and resid 32 through 46 Processing helix chain 'AJ' and resid 46 through 62 removed outlier: 3.587A pdb=" N VALAJ 51 " --> pdb=" O ARGAJ 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYSAJ 52 " --> pdb=" O GLUAJ 48 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 74 through 99 Processing helix chain 'AJ' and resid 101 through 109 Processing helix chain 'AJ' and resid 111 through 120 Processing helix chain 'AJ' and resid 122 through 139 removed outlier: 3.526A pdb=" N VALAJ 126 " --> pdb=" O PROAJ 122 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 142 through 161 removed outlier: 3.812A pdb=" N ALAAJ 151 " --> pdb=" O ALAAJ 147 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYRAJ 152 " --> pdb=" O GLUAJ 148 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VALAJ 156 " --> pdb=" O TYRAJ 152 " (cutoff:3.500A) Processing helix chain 'AK' and resid 3 through 16 removed outlier: 3.883A pdb=" N THRAK 15 " --> pdb=" O ASNAK 11 " (cutoff:3.500A) Processing helix chain 'AK' and resid 20 through 47 removed outlier: 4.409A pdb=" N SERAK 35 " --> pdb=" O PHEAK 31 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALAAK 36 " --> pdb=" O GLUAK 32 " (cutoff:3.500A) Processing helix chain 'AK' and resid 47 through 63 removed outlier: 3.639A pdb=" N VALAK 52 " --> pdb=" O SERAK 48 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLUAK 61 " --> pdb=" O ALAAK 57 " (cutoff:3.500A) Processing helix chain 'AK' and resid 75 through 100 removed outlier: 3.826A pdb=" N ILEAK 98 " --> pdb=" O SERAK 94 " (cutoff:3.500A) Processing helix chain 'AK' and resid 102 through 108 removed outlier: 3.544A pdb=" N ARGAK 108 " --> pdb=" O VALAK 104 " (cutoff:3.500A) Processing helix chain 'AK' and resid 113 through 121 Processing helix chain 'AK' and resid 124 through 145 removed outlier: 3.627A pdb=" N VALAK 128 " --> pdb=" O ILEAK 124 " (cutoff:3.500A) Processing helix chain 'AK' and resid 150 through 152 No H-bonds generated for 'chain 'AK' and resid 150 through 152' Processing helix chain 'AK' and resid 153 through 165 removed outlier: 4.488A pdb=" N PHEAK 157 " --> pdb=" O ILEAK 153 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEUAK 164 " --> pdb=" O METAK 160 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 16 Processing helix chain 'AL' and resid 21 through 47 removed outlier: 3.578A pdb=" N LYSAL 26 " --> pdb=" O ALAAL 22 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLUAL 35 " --> pdb=" O PHEAL 31 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEUAL 36 " --> pdb=" O ALAAL 32 " (cutoff:3.500A) Processing helix chain 'AL' and resid 47 through 60 removed outlier: 3.744A pdb=" N VALAL 52 " --> pdb=" O ALAAL 48 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYSAL 53 " --> pdb=" O ALAAL 49 " (cutoff:3.500A) Processing helix chain 'AL' and resid 74 through 99 Processing helix chain 'AL' and resid 101 through 107 Processing helix chain 'AL' and resid 111 through 120 removed outlier: 3.741A pdb=" N SERAL 118 " --> pdb=" O GLUAL 114 " (cutoff:3.500A) Processing helix chain 'AL' and resid 122 through 141 Processing helix chain 'AL' and resid 142 through 161 removed outlier: 4.586A pdb=" N TYRAL 152 " --> pdb=" O GLUAL 148 " (cutoff:3.500A) Processing helix chain 'AN' and resid 3 through 14 Processing helix chain 'AN' and resid 19 through 32 Processing helix chain 'AN' and resid 32 through 46 removed outlier: 3.521A pdb=" N ILEAN 39 " --> pdb=" O ALAAN 35 " (cutoff:3.500A) Processing helix chain 'AN' and resid 49 through 62 Processing helix chain 'AN' and resid 74 through 99 Processing helix chain 'AN' and resid 101 through 109 removed outlier: 4.890A pdb=" N ILEAN 107 " --> pdb=" O PROAN 103 " (cutoff:3.500A) Processing helix chain 'AN' and resid 112 through 120 removed outlier: 3.745A pdb=" N SERAN 118 " --> pdb=" O GLUAN 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEUAN 119 " --> pdb=" O METAN 115 " (cutoff:3.500A) Processing helix chain 'AN' and resid 122 through 140 Processing helix chain 'AN' and resid 143 through 161 removed outlier: 3.714A pdb=" N ALAAN 147 " --> pdb=" O SERAN 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLUAN 148 " --> pdb=" O ASPAN 144 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYRAN 152 " --> pdb=" O GLUAN 148 " (cutoff:3.500A) Processing helix chain 'AO' and resid 3 through 16 removed outlier: 3.617A pdb=" N VALAO 8 " --> pdb=" O ALAAO 4 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLNAO 15 " --> pdb=" O SERAO 11 " (cutoff:3.500A) Processing helix chain 'AO' and resid 20 through 47 removed outlier: 4.028A pdb=" N GLUAO 35 " --> pdb=" O PHEAO 31 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEUAO 36 " --> pdb=" O ALAAO 32 " (cutoff:3.500A) Processing helix chain 'AO' and resid 48 through 60 removed outlier: 3.650A pdb=" N VALAO 52 " --> pdb=" O ALAAO 48 " (cutoff:3.500A) Processing helix chain 'AO' and resid 74 through 99 Processing helix chain 'AO' and resid 101 through 107 Processing helix chain 'AO' and resid 111 through 120 Processing helix chain 'AO' and resid 122 through 141 Processing helix chain 'AO' and resid 144 through 160 removed outlier: 4.306A pdb=" N TYRAO 152 " --> pdb=" O GLUAO 148 " (cutoff:3.500A) Processing helix chain 'AP' and resid 3 through 14 Processing helix chain 'AP' and resid 19 through 32 Processing helix chain 'AP' and resid 33 through 46 Processing helix chain 'AP' and resid 46 through 62 removed outlier: 3.533A pdb=" N LYSAP 52 " --> pdb=" O GLUAP 48 " (cutoff:3.500A) Processing helix chain 'AP' and resid 74 through 99 removed outlier: 3.611A pdb=" N ALAAP 79 " --> pdb=" O GLUAP 75 " (cutoff:3.500A) Processing helix chain 'AP' and resid 101 through 109 removed outlier: 3.525A pdb=" N GLUAP 105 " --> pdb=" O VALAP 101 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEUAP 109 " --> pdb=" O GLUAP 105 " (cutoff:3.500A) Processing helix chain 'AP' and resid 112 through 120 Processing helix chain 'AP' and resid 122 through 139 removed outlier: 3.557A pdb=" N VALAP 126 " --> pdb=" O PROAP 122 " (cutoff:3.500A) Processing helix chain 'AP' and resid 142 through 161 removed outlier: 3.693A pdb=" N ALAAP 151 " --> pdb=" O ALAAP 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYRAP 152 " --> pdb=" O GLUAP 148 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHEAP 155 " --> pdb=" O ALAAP 151 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 3 through 16 Processing helix chain 'AQ' and resid 20 through 33 removed outlier: 3.554A pdb=" N TYRAQ 30 " --> pdb=" O LYSAQ 26 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 33 through 47 Processing helix chain 'AQ' and resid 47 through 60 removed outlier: 3.841A pdb=" N VALAQ 52 " --> pdb=" O ALAAQ 48 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSAQ 58 " --> pdb=" O GLUAQ 54 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 74 through 99 Processing helix chain 'AQ' and resid 101 through 108 removed outlier: 3.623A pdb=" N ASPAQ 105 " --> pdb=" O ALAAQ 101 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 112 through 120 Processing helix chain 'AQ' and resid 122 through 141 Processing helix chain 'AQ' and resid 143 through 161 removed outlier: 3.895A pdb=" N TYRAQ 152 " --> pdb=" O GLUAQ 148 " (cutoff:3.500A) Processing helix chain 'AR' and resid 3 through 14 removed outlier: 3.648A pdb=" N GLUAR 14 " --> pdb=" O ASNAR 10 " (cutoff:3.500A) Processing helix chain 'AR' and resid 19 through 32 Processing helix chain 'AR' and resid 33 through 46 Processing helix chain 'AR' and resid 46 through 62 removed outlier: 3.664A pdb=" N VALAR 51 " --> pdb=" O ARGAR 47 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSAR 52 " --> pdb=" O GLUAR 48 " (cutoff:3.500A) Processing helix chain 'AR' and resid 74 through 99 Processing helix chain 'AR' and resid 101 through 109 Processing helix chain 'AR' and resid 111 through 120 Processing helix chain 'AR' and resid 122 through 141 removed outlier: 3.569A pdb=" N VALAR 126 " --> pdb=" O PROAR 122 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLUAR 135 " --> pdb=" O ARGAR 131 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEUAR 140 " --> pdb=" O VALAR 136 " (cutoff:3.500A) Processing helix chain 'AR' and resid 142 through 148 removed outlier: 3.728A pdb=" N GLUAR 148 " --> pdb=" O ASPAR 144 " (cutoff:3.500A) Processing helix chain 'AR' and resid 149 through 161 removed outlier: 3.939A pdb=" N PHEAR 153 " --> pdb=" O ALAAR 149 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VALAR 156 " --> pdb=" O TYRAR 152 " (cutoff:3.500A) Processing helix chain 'AS' and resid 3 through 16 removed outlier: 3.529A pdb=" N VALAS 8 " --> pdb=" O ALAAS 4 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLNAS 15 " --> pdb=" O SERAS 11 " (cutoff:3.500A) Processing helix chain 'AS' and resid 20 through 33 removed outlier: 3.604A pdb=" N SERAS 33 " --> pdb=" O SERAS 29 " (cutoff:3.500A) Processing helix chain 'AS' and resid 34 through 47 removed outlier: 3.504A pdb=" N VALAS 43 " --> pdb=" O ARGAS 39 " (cutoff:3.500A) Processing helix chain 'AS' and resid 47 through 60 removed outlier: 4.039A pdb=" N VALAS 52 " --> pdb=" O ALAAS 48 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SERAS 59 " --> pdb=" O ALAAS 55 " (cutoff:3.500A) Processing helix chain 'AS' and resid 74 through 99 Processing helix chain 'AS' and resid 102 through 108 Processing helix chain 'AS' and resid 112 through 120 Processing helix chain 'AS' and resid 122 through 142 removed outlier: 3.708A pdb=" N GLUAS 135 " --> pdb=" O GLNAS 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VALAS 136 " --> pdb=" O ALAAS 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEUAS 140 " --> pdb=" O VALAS 136 " (cutoff:3.500A) Processing helix chain 'AS' and resid 143 through 161 removed outlier: 3.597A pdb=" N TYRAS 152 " --> pdb=" O GLUAS 148 " (cutoff:3.500A) Processing helix chain 'AU' and resid 3 through 14 removed outlier: 3.616A pdb=" N GLUAU 14 " --> pdb=" O ASNAU 10 " (cutoff:3.500A) Processing helix chain 'AU' and resid 19 through 32 Processing helix chain 'AU' and resid 32 through 46 Processing helix chain 'AU' and resid 46 through 62 removed outlier: 3.665A pdb=" N VALAU 51 " --> pdb=" O ARGAU 47 " (cutoff:3.500A) Processing helix chain 'AU' and resid 63 through 66 Processing helix chain 'AU' and resid 74 through 99 removed outlier: 3.595A pdb=" N ALAAU 79 " --> pdb=" O GLUAU 75 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VALAU 97 " --> pdb=" O THRAU 93 " (cutoff:3.500A) Processing helix chain 'AU' and resid 101 through 109 removed outlier: 3.527A pdb=" N LEUAU 109 " --> pdb=" O GLUAU 105 " (cutoff:3.500A) Processing helix chain 'AU' and resid 111 through 120 removed outlier: 3.623A pdb=" N ARGAU 117 " --> pdb=" O ARGAU 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEUAU 119 " --> pdb=" O METAU 115 " (cutoff:3.500A) Processing helix chain 'AU' and resid 122 through 141 removed outlier: 3.634A pdb=" N VALAU 126 " --> pdb=" O PROAU 122 " (cutoff:3.500A) Processing helix chain 'AU' and resid 142 through 161 removed outlier: 3.873A pdb=" N GLUAU 148 " --> pdb=" O ASPAU 144 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAU 151 " --> pdb=" O ALAAU 147 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYRAU 152 " --> pdb=" O GLUAU 148 " (cutoff:3.500A) Processing helix chain 'AV' and resid 3 through 16 removed outlier: 3.901A pdb=" N GLNAV 15 " --> pdb=" O SERAV 11 " (cutoff:3.500A) Processing helix chain 'AV' and resid 20 through 33 removed outlier: 3.646A pdb=" N LYSAV 26 " --> pdb=" O ALAAV 22 " (cutoff:3.500A) Processing helix chain 'AV' and resid 33 through 47 Processing helix chain 'AV' and resid 47 through 60 removed outlier: 3.801A pdb=" N ILEAV 51 " --> pdb=" O ASNAV 47 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VALAV 52 " --> pdb=" O ALAAV 48 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAV 56 " --> pdb=" O VALAV 52 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALAAV 57 " --> pdb=" O LYSAV 53 " (cutoff:3.500A) Processing helix chain 'AV' and resid 74 through 99 Processing helix chain 'AV' and resid 103 through 108 Processing helix chain 'AV' and resid 112 through 119 Processing helix chain 'AV' and resid 122 through 141 removed outlier: 3.586A pdb=" N THRAV 126 " --> pdb=" O PROAV 122 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLUAV 135 " --> pdb=" O GLNAV 131 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VALAV 136 " --> pdb=" O ALAAV 132 " (cutoff:3.500A) Processing helix chain 'AV' and resid 142 through 161 removed outlier: 3.744A pdb=" N TYRAV 152 " --> pdb=" O GLUAV 148 " (cutoff:3.500A) Processing helix chain 'AW' and resid 3 through 14 removed outlier: 3.673A pdb=" N GLUAW 14 " --> pdb=" O ASNAW 10 " (cutoff:3.500A) Processing helix chain 'AW' and resid 19 through 32 Processing helix chain 'AW' and resid 32 through 46 Processing helix chain 'AW' and resid 46 through 62 removed outlier: 3.528A pdb=" N VALAW 51 " --> pdb=" O ARGAW 47 " (cutoff:3.500A) Processing helix chain 'AW' and resid 74 through 99 removed outlier: 3.600A pdb=" N VALAW 97 " --> pdb=" O THRAW 93 " (cutoff:3.500A) Processing helix chain 'AW' and resid 101 through 109 removed outlier: 3.559A pdb=" N ILEAW 107 " --> pdb=" O PROAW 103 " (cutoff:3.500A) Processing helix chain 'AW' and resid 114 through 120 removed outlier: 3.556A pdb=" N SERAW 118 " --> pdb=" O GLUAW 114 " (cutoff:3.500A) Processing helix chain 'AW' and resid 122 through 141 Processing helix chain 'AW' and resid 142 through 161 removed outlier: 4.177A pdb=" N GLUAW 148 " --> pdb=" O ASPAW 144 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALAAW 151 " --> pdb=" O ALAAW 147 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYRAW 152 " --> pdb=" O GLUAW 148 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHEAW 155 " --> pdb=" O ALAAW 151 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VALAW 156 " --> pdb=" O TYRAW 152 " (cutoff:3.500A) Processing helix chain 'AX' and resid 4 through 16 removed outlier: 4.167A pdb=" N GLNAX 15 " --> pdb=" O SERAX 11 " (cutoff:3.500A) Processing helix chain 'AX' and resid 20 through 47 removed outlier: 4.206A pdb=" N LYSAX 26 " --> pdb=" O ALAAX 22 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEUAX 27 " --> pdb=" O ALAAX 23 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLUAX 35 " --> pdb=" O PHEAX 31 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEUAX 36 " --> pdb=" O ALAAX 32 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARGAX 39 " --> pdb=" O GLUAX 35 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VALAX 43 " --> pdb=" O ARGAX 39 " (cutoff:3.500A) Processing helix chain 'AX' and resid 47 through 60 removed outlier: 3.680A pdb=" N VALAX 52 " --> pdb=" O ALAAX 48 " (cutoff:3.500A) Processing helix chain 'AX' and resid 74 through 99 Processing helix chain 'AX' and resid 101 through 108 removed outlier: 3.603A pdb=" N ASPAX 105 " --> pdb=" O ALAAX 101 " (cutoff:3.500A) Processing helix chain 'AX' and resid 112 through 120 Processing helix chain 'AX' and resid 122 through 142 Processing helix chain 'AX' and resid 142 through 161 removed outlier: 4.319A pdb=" N TYRAX 152 " --> pdb=" O GLUAX 148 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYSAX 157 " --> pdb=" O LEUAX 153 " (cutoff:3.500A) Processing helix chain 'AY' and resid 3 through 14 removed outlier: 3.601A pdb=" N GLUAY 14 " --> pdb=" O ASNAY 10 " (cutoff:3.500A) Processing helix chain 'AY' and resid 19 through 32 Processing helix chain 'AY' and resid 32 through 46 removed outlier: 3.584A pdb=" N ARGAY 36 " --> pdb=" O GLYAY 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILEAY 39 " --> pdb=" O ALAAY 35 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALAAY 40 " --> pdb=" O ARGAY 36 " (cutoff:3.500A) Processing helix chain 'AY' and resid 46 through 62 removed outlier: 3.754A pdb=" N ILEAY 50 " --> pdb=" O SERAY 46 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VALAY 51 " --> pdb=" O ARGAY 47 " (cutoff:3.500A) Processing helix chain 'AY' and resid 74 through 99 Processing helix chain 'AY' and resid 101 through 109 removed outlier: 3.625A pdb=" N ILEAY 107 " --> pdb=" O PROAY 103 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLYAY 108 " --> pdb=" O ILEAY 104 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEUAY 109 " --> pdb=" O GLUAY 105 " (cutoff:3.500A) Processing helix chain 'AY' and resid 111 through 120 removed outlier: 3.679A pdb=" N METAY 115 " --> pdb=" O GLYAY 111 " (cutoff:3.500A) Processing helix chain 'AY' and resid 122 through 140 Processing helix chain 'AY' and resid 142 through 161 removed outlier: 3.808A pdb=" N ALAAY 151 " --> pdb=" O ALAAY 147 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYRAY 152 " --> pdb=" O GLUAY 148 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHEAY 155 " --> pdb=" O ALAAY 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAY 156 " --> pdb=" O TYRAY 152 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 3 through 16 removed outlier: 3.773A pdb=" N GLNAZ 15 " --> pdb=" O SERAZ 11 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 20 through 47 removed outlier: 3.541A pdb=" N LYSAZ 26 " --> pdb=" O ALAAZ 22 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLUAZ 35 " --> pdb=" O PHEAZ 31 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEUAZ 36 " --> pdb=" O ALAAZ 32 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 47 through 60 removed outlier: 3.794A pdb=" N VALAZ 52 " --> pdb=" O ALAAZ 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALAAZ 57 " --> pdb=" O LYSAZ 53 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 74 through 99 Processing helix chain 'AZ' and resid 102 through 107 Processing helix chain 'AZ' and resid 111 through 120 removed outlier: 3.546A pdb=" N THRAZ 115 " --> pdb=" O GLYAZ 111 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 122 through 142 removed outlier: 3.579A pdb=" N THRAZ 126 " --> pdb=" O PROAZ 122 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLUAZ 135 " --> pdb=" O GLNAZ 131 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 142 through 161 removed outlier: 3.852A pdb=" N GLUAZ 148 " --> pdb=" O ASPAZ 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYRAZ 152 " --> pdb=" O GLUAZ 148 " (cutoff:3.500A) Processing helix chain 'BB' and resid 14 through 19 Processing helix chain 'BB' and resid 33 through 46 removed outlier: 4.479A pdb=" N PHEBB 37 " --> pdb=" O TYRBB 33 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARGBB 38 " --> pdb=" O ASPBB 34 " (cutoff:3.500A) Processing helix chain 'BC' and resid 21 through 25 Processing helix chain 'BC' and resid 35 through 47 Processing helix chain 'BE' and resid 19 through 30 removed outlier: 3.658A pdb=" N GLNBE 27 " --> pdb=" O SERBE 23 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALABE 28 " --> pdb=" O ALABE 24 " (cutoff:3.500A) Processing helix chain 'BE' and resid 36 through 63 removed outlier: 3.611A pdb=" N ASNBE 41 " --> pdb=" O GLYBE 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEUBE 43 " --> pdb=" O GLUBE 39 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYRBE 46 " --> pdb=" O GLUBE 42 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALABE 51 " --> pdb=" O PHEBE 47 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEUBE 52 " --> pdb=" O GLNBE 48 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLUBE 55 " --> pdb=" O ALABE 51 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THRBE 59 " --> pdb=" O GLUBE 55 " (cutoff:3.500A) Processing helix chain 'BE' and resid 63 through 75 removed outlier: 3.625A pdb=" N ARGBE 74 " --> pdb=" O ARGBE 70 " (cutoff:3.500A) Processing helix chain 'BE' and resid 80 through 84 removed outlier: 3.598A pdb=" N SERBE 83 " --> pdb=" O SERBE 80 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYRBE 84 " --> pdb=" O PROBE 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 80 through 84' Processing helix chain 'BE' and resid 141 through 145 removed outlier: 3.546A pdb=" N GLYBE 145 " --> pdb=" O ILEBE 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 141 through 145' Processing helix chain 'BE' and resid 145 through 170 removed outlier: 3.602A pdb=" N LEUBE 160 " --> pdb=" O METBE 156 " (cutoff:3.500A) Processing helix chain 'BE' and resid 172 through 181 removed outlier: 3.717A pdb=" N ASNBE 178 " --> pdb=" O ILEBE 174 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLYBE 181 " --> pdb=" O VALBE 177 " (cutoff:3.500A) Processing helix chain 'BE' and resid 182 through 188 removed outlier: 4.241A pdb=" N ASNBE 188 " --> pdb=" O GLUBE 184 " (cutoff:3.500A) Processing helix chain 'BE' and resid 191 through 211 removed outlier: 3.623A pdb=" N THRBE 195 " --> pdb=" O SERBE 191 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VALBE 197 " --> pdb=" O ASPBE 193 " (cutoff:3.500A) Processing helix chain 'BE' and resid 213 through 233 removed outlier: 3.887A pdb=" N GLUBE 218 " --> pdb=" O ALABE 214 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILEBE 219 " --> pdb=" O GLNBE 215 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VALBE 220 " --> pdb=" O ALABE 216 " (cutoff:3.500A) Processing helix chain 'BE' and resid 274 through 290 Processing helix chain 'BE' and resid 293 through 298 Processing helix chain 'BE' and resid 302 through 312 removed outlier: 4.067A pdb=" N GLNBE 308 " --> pdb=" O TYRBE 304 " (cutoff:3.500A) Processing helix chain 'BE' and resid 315 through 325 Processing helix chain 'BE' and resid 326 through 334 removed outlier: 4.058A pdb=" N GLNBE 332 " --> pdb=" O LEUBE 328 " (cutoff:3.500A) Processing helix chain 'BE' and resid 338 through 351 removed outlier: 3.751A pdb=" N ARGBE 348 " --> pdb=" O GLUBE 344 " (cutoff:3.500A) Processing helix chain 'BE' and resid 357 through 371 Processing helix chain 'BE' and resid 372 through 382 Processing helix chain 'BE' and resid 385 through 390 Processing helix chain 'BE' and resid 410 through 416 Processing helix chain 'BE' and resid 421 through 425 removed outlier: 3.784A pdb=" N PHEBE 424 " --> pdb=" O SERBE 421 " (cutoff:3.500A) Processing helix chain 'BE' and resid 429 through 439 removed outlier: 3.516A pdb=" N THRBE 433 " --> pdb=" O GLNBE 429 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASPBE 438 " --> pdb=" O PHEBE 434 " (cutoff:3.500A) Processing helix chain 'BE' and resid 489 through 493 removed outlier: 3.757A pdb=" N ASNBE 493 " --> pdb=" O ALABE 490 " (cutoff:3.500A) Processing helix chain 'BE' and resid 536 through 551 Processing helix chain 'BE' and resid 556 through 560 removed outlier: 3.726A pdb=" N GLNBE 559 " --> pdb=" O TYRBE 556 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARGBE 560 " --> pdb=" O GLUBE 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 556 through 560' Processing helix chain 'BE' and resid 561 through 570 Processing helix chain 'BE' and resid 574 through 584 Processing helix chain 'BE' and resid 585 through 592 Processing helix chain 'BE' and resid 597 through 610 Processing helix chain 'BE' and resid 616 through 630 removed outlier: 3.566A pdb=" N GLNBE 622 " --> pdb=" O GLNBE 618 " (cutoff:3.500A) Processing helix chain 'BE' and resid 631 through 641 Processing helix chain 'BE' and resid 642 through 649 Processing helix chain 'BE' and resid 661 through 669 Processing helix chain 'BG' and resid 195 through 202 removed outlier: 4.212A pdb=" N GLUBG 199 " --> pdb=" O VALBG 195 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARGBG 201 " --> pdb=" O GLNBG 197 " (cutoff:3.500A) Processing helix chain 'BG' and resid 220 through 225 removed outlier: 3.649A pdb=" N SERBG 224 " --> pdb=" O GLYBG 220 " (cutoff:3.500A) Processing helix chain 'BG' and resid 241 through 246 removed outlier: 3.650A pdb=" N VALBG 246 " --> pdb=" O ILEBG 242 " (cutoff:3.500A) Processing helix chain 'BH' and resid 20 through 31 removed outlier: 3.602A pdb=" N LEUBH 31 " --> pdb=" O ARGBH 27 " (cutoff:3.500A) Processing helix chain 'BH' and resid 32 through 46 removed outlier: 3.604A pdb=" N TRPBH 41 " --> pdb=" O LEUBH 37 " (cutoff:3.500A) Processing helix chain 'BH' and resid 64 through 74 removed outlier: 3.628A pdb=" N METBH 74 " --> pdb=" O GLUBH 70 " (cutoff:3.500A) Processing helix chain 'BH' and resid 75 through 89 removed outlier: 3.657A pdb=" N THRBH 80 " --> pdb=" O PROBH 76 " (cutoff:3.500A) Processing helix chain 'BH' and resid 92 through 99 Processing helix chain 'BH' and resid 102 through 120 Processing helix chain 'BH' and resid 132 through 145 removed outlier: 3.503A pdb=" N VALBH 138 " --> pdb=" O ASNBH 134 " (cutoff:3.500A) Processing helix chain 'BH' and resid 146 through 160 removed outlier: 3.669A pdb=" N ILEBH 151 " --> pdb=" O SERBH 147 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THRBH 152 " --> pdb=" O GLYBH 148 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASPBH 160 " --> pdb=" O ASNBH 156 " (cutoff:3.500A) Processing helix chain 'BI' and resid 104 through 106 No H-bonds generated for 'chain 'BI' and resid 104 through 106' Processing helix chain 'BI' and resid 107 through 117 Processing sheet with id=AA1, first strand: chain 'BB' and resid 26 through 32 removed outlier: 6.845A pdb=" N CYSBB 9 " --> pdb=" O ILEBB 50 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILEBB 50 " --> pdb=" O CYSBB 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'BC' and resid 26 through 32 removed outlier: 7.040A pdb=" N METBC 3 " --> pdb=" O LEUBC 55 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEUBC 55 " --> pdb=" O METBC 3 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ARGBC 5 " --> pdb=" O VALBC 53 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VALBC 53 " --> pdb=" O ARGBC 5 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THRBC 7 " --> pdb=" O VALBC 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'BE' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'BE' and resid 239 through 241 Processing sheet with id=AA5, first strand: chain 'BE' and resid 485 through 486 Processing sheet with id=AA6, first strand: chain 'BE' and resid 513 through 514 removed outlier: 4.510A pdb=" N PHEBE 513 " --> pdb=" O VALBE 654 " (cutoff:3.500A) 2490 hydrogen bonds defined for protein. 7446 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: 7.29 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7228 1.33 - 1.45: 8780 1.45 - 1.57: 21461 1.57 - 1.70: 1 1.70 - 1.82: 347 Bond restraints: 37817 Sorted by residual: bond pdb=" C34 45DBH 400 " pdb=" C36 45DBH 400 " ideal model delta sigma weight residual 1.444 1.539 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C4A CYCAW 200 " pdb=" CHB CYCAW 200 " ideal model delta sigma weight residual 1.437 1.371 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C4A CYCAK 200 " pdb=" CHB CYCAK 200 " ideal model delta sigma weight residual 1.437 1.371 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C4A CYCAI 200 " pdb=" CHB CYCAI 200 " ideal model delta sigma weight residual 1.437 1.374 0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" C4A CYCAJ 200 " pdb=" CHB CYCAJ 200 " ideal model delta sigma weight residual 1.437 1.374 0.063 2.00e-02 2.50e+03 9.96e+00 ... (remaining 37812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 41227 1.82 - 3.63: 8888 3.63 - 5.45: 1088 5.45 - 7.26: 28 7.26 - 9.08: 26 Bond angle restraints: 51257 Sorted by residual: angle pdb=" N PHEBE 424 " pdb=" CA PHEBE 424 " pdb=" C PHEBE 424 " ideal model delta sigma weight residual 114.62 108.84 5.78 1.14e+00 7.69e-01 2.57e+01 angle pdb=" C SERAL 33 " pdb=" N GLYAL 34 " pdb=" CA GLYAL 34 " ideal model delta sigma weight residual 120.03 125.06 -5.03 1.12e+00 7.97e-01 2.02e+01 angle pdb=" C METAL 149 " pdb=" N GLYAL 150 " pdb=" CA GLYAL 150 " ideal model delta sigma weight residual 119.98 124.56 -4.58 1.11e+00 8.12e-01 1.70e+01 angle pdb=" C SERAK 33 " pdb=" N GLYAK 34 " pdb=" CA GLYAK 34 " ideal model delta sigma weight residual 119.98 124.55 -4.57 1.11e+00 8.12e-01 1.70e+01 angle pdb=" C ILEAC 157 " pdb=" N GLYAC 158 " pdb=" CA GLYAC 158 " ideal model delta sigma weight residual 119.98 124.48 -4.50 1.11e+00 8.12e-01 1.65e+01 ... (remaining 51252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 20072 17.44 - 34.88: 2569 34.88 - 52.33: 450 52.33 - 69.77: 265 69.77 - 87.21: 73 Dihedral angle restraints: 23429 sinusoidal: 9721 harmonic: 13708 Sorted by residual: dihedral pdb=" C THRBH 15 " pdb=" N THRBH 15 " pdb=" CA THRBH 15 " pdb=" CB THRBH 15 " ideal model delta harmonic sigma weight residual -122.00 -132.94 10.94 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C THRAW 102 " pdb=" N THRAW 102 " pdb=" CA THRAW 102 " pdb=" CB THRAW 102 " ideal model delta harmonic sigma weight residual -122.00 -132.47 10.47 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" C THRAN 102 " pdb=" N THRAN 102 " pdb=" CA THRAN 102 " pdb=" CB THRAN 102 " ideal model delta harmonic sigma weight residual -122.00 -132.11 10.11 0 2.50e+00 1.60e-01 1.63e+01 ... (remaining 23426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3369 0.067 - 0.135: 1823 0.135 - 0.202: 393 0.202 - 0.269: 138 0.269 - 0.337: 17 Chirality restraints: 5740 Sorted by residual: chirality pdb=" CA THRBH 15 " pdb=" N THRBH 15 " pdb=" C THRBH 15 " pdb=" CB THRBH 15 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA THRBE 528 " pdb=" N THRBE 528 " pdb=" C THRBE 528 " pdb=" CB THRBE 528 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA THRAW 102 " pdb=" N THRAW 102 " pdb=" C THRAW 102 " pdb=" CB THRAW 102 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 5737 not shown) Planarity restraints: 6586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CYCAX 200 " -0.076 2.00e-02 2.50e+03 2.70e-01 1.64e+03 pdb=" C2A CYCAX 200 " 0.115 2.00e-02 2.50e+03 pdb=" C3A CYCAX 200 " -0.113 2.00e-02 2.50e+03 pdb=" C4A CYCAX 200 " 0.079 2.00e-02 2.50e+03 pdb=" CAA CYCAX 200 " 0.470 2.00e-02 2.50e+03 pdb=" CHA CYCAX 200 " -0.304 2.00e-02 2.50e+03 pdb=" CHB CYCAX 200 " 0.297 2.00e-02 2.50e+03 pdb=" CMA CYCAX 200 " -0.466 2.00e-02 2.50e+03 pdb=" NA CYCAX 200 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAA 200 " 0.269 2.00e-02 2.50e+03 2.60e-01 1.52e+03 pdb=" OB CYCAA 200 " 0.072 2.00e-02 2.50e+03 pdb=" C1B CYCAA 200 " -0.039 2.00e-02 2.50e+03 pdb=" C2B CYCAA 200 " 0.120 2.00e-02 2.50e+03 pdb=" C3B CYCAA 200 " -0.068 2.00e-02 2.50e+03 pdb=" C4B CYCAA 200 " 0.093 2.00e-02 2.50e+03 pdb=" CAB CYCAA 200 " -0.392 2.00e-02 2.50e+03 pdb=" CHB CYCAA 200 " -0.444 2.00e-02 2.50e+03 pdb=" CMB CYCAA 200 " 0.390 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAY 200 " 0.290 2.00e-02 2.50e+03 2.41e-01 1.30e+03 pdb=" OB CYCAY 200 " 0.029 2.00e-02 2.50e+03 pdb=" C1B CYCAY 200 " -0.029 2.00e-02 2.50e+03 pdb=" C2B CYCAY 200 " 0.109 2.00e-02 2.50e+03 pdb=" C3B CYCAY 200 " -0.057 2.00e-02 2.50e+03 pdb=" C4B CYCAY 200 " 0.085 2.00e-02 2.50e+03 pdb=" CAB CYCAY 200 " -0.344 2.00e-02 2.50e+03 pdb=" CHB CYCAY 200 " -0.424 2.00e-02 2.50e+03 pdb=" CMB CYCAY 200 " 0.340 2.00e-02 2.50e+03 ... (remaining 6583 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 13811 2.95 - 3.44: 41435 3.44 - 3.93: 66332 3.93 - 4.41: 75496 4.41 - 4.90: 124742 Nonbonded interactions: 321816 Sorted by model distance: nonbonded pdb=" O ILEBE 192 " pdb=" OG1 THRBE 195 " model vdw 2.465 3.040 nonbonded pdb=" O ASNBG 241 " pdb=" OG SERBG 245 " model vdw 2.487 3.040 nonbonded pdb=" OG1 THRAW 5 " pdb=" OD2 ASPAX 3 " model vdw 2.509 3.040 nonbonded pdb=" O ARGBE 161 " pdb=" OG1 THRBE 164 " model vdw 2.532 3.040 nonbonded pdb=" O PHEBE 159 " pdb=" OG1 THRBE 163 " model vdw 2.551 3.040 ... (remaining 321811 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 'AA' selection = chain 'AC' selection = chain 'AH' selection = chain 'AJ' selection = chain 'AN' selection = chain 'AP' selection = chain 'AR' selection = chain 'AU' selection = chain 'AW' selection = chain 'AY' } ncs_group { reference = chain 'AB' selection = chain 'AD' selection = chain 'AF' selection = chain 'AI' selection = chain 'AL' selection = chain 'AO' selection = chain 'AQ' selection = chain 'AS' selection = chain 'AV' selection = chain 'AX' selection = chain 'AZ' } ncs_group { reference = chain 'BB' selection = chain 'BC' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.190 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 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:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 0.095 37841 Z= 0.507 Angle : 1.514 9.078 51257 Z= 1.025 Chirality : 0.085 0.337 5740 Planarity : 0.016 0.270 6586 Dihedral : 17.111 87.212 14695 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.57 % Favored : 96.22 % Rotamer: Outliers : 2.69 % Allowed : 9.39 % Favored : 87.92 % Cbeta Deviations : 0.07 % 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: -4.74 (0.08), residues: 4683 helix: -3.07 (0.06), residues: 3608 sheet: -0.95 (0.73), residues: 46 loop : -2.43 (0.16), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAQ 83 TYR 0.022 0.002 TYRBE 597 PHE 0.015 0.002 PHEBE 424 TRP 0.012 0.002 TRPBE 158 HIS 0.002 0.001 HISAE 62 Details of bonding type rmsd covalent geometry : bond 0.00743 (37817) covalent geometry : angle 1.51408 (51257) hydrogen bonds : bond 0.28162 ( 2490) hydrogen bonds : angle 9.66851 ( 7446) Misc. bond : bond 0.07546 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 878 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 6 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8652 (mtpt) REVERT: AA 10 ASN cc_start: 0.8892 (m110) cc_final: 0.8682 (m110) REVERT: AA 49 THR cc_start: 0.9178 (p) cc_final: 0.8967 (p) REVERT: AA 64 ASP cc_start: 0.9196 (p0) cc_final: 0.8961 (p0) REVERT: AA 105 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7720 (mm-30) REVERT: AA 128 GLN cc_start: 0.8466 (tp-100) cc_final: 0.8190 (tp40) REVERT: AB 10 ASN cc_start: 0.8834 (t0) cc_final: 0.8392 (t0) REVERT: AB 13 ASP cc_start: 0.8477 (t70) cc_final: 0.8086 (t0) REVERT: AB 100 ASP cc_start: 0.7911 (t70) cc_final: 0.7662 (t0) REVERT: AB 157 CYS cc_start: 0.8703 (m) cc_final: 0.8297 (m) REVERT: AC 24 ASP cc_start: 0.8198 (m-30) cc_final: 0.7694 (t0) REVERT: AC 27 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8653 (tmmt) REVERT: AC 52 LYS cc_start: 0.8801 (tptp) cc_final: 0.8129 (tppt) REVERT: AC 60 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8388 (tm-30) REVERT: AC 61 LYS cc_start: 0.9160 (ttmm) cc_final: 0.8865 (ttmm) REVERT: AC 124 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: AC 141 MET cc_start: 0.7582 (ptp) cc_final: 0.7173 (ptt) REVERT: AD 2 GLN cc_start: 0.8112 (pm20) cc_final: 0.7729 (pm20) REVERT: AD 37 ARG cc_start: 0.9043 (mtt90) cc_final: 0.8731 (mtp85) REVERT: AD 71 ASN cc_start: 0.6685 (t0) cc_final: 0.6253 (t0) REVERT: AD 117 ASN cc_start: 0.9052 (m110) cc_final: 0.8851 (m-40) REVERT: AD 131 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7369 (tm-30) REVERT: AE 14 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8715 (mp10) REVERT: AE 37 ILE cc_start: 0.8908 (mt) cc_final: 0.8697 (mm) REVERT: AE 60 LYS cc_start: 0.9199 (ttpp) cc_final: 0.8908 (tmmm) REVERT: AE 128 ASP cc_start: 0.8701 (m-30) cc_final: 0.8445 (m-30) REVERT: AF 17 LYS cc_start: 0.7739 (mtmp) cc_final: 0.7518 (mtmm) REVERT: AF 71 ASN cc_start: 0.8580 (t0) cc_final: 0.8308 (t0) REVERT: AF 86 ASP cc_start: 0.7771 (t70) cc_final: 0.7513 (t0) REVERT: AF 100 ASP cc_start: 0.7632 (t70) cc_final: 0.7285 (t0) REVERT: AF 131 GLN cc_start: 0.8232 (mm110) cc_final: 0.7893 (mm-40) REVERT: AI 2 GLN cc_start: 0.7764 (mt0) cc_final: 0.7520 (mt0) REVERT: AJ 52 LYS cc_start: 0.8404 (tmtm) cc_final: 0.7995 (tptp) REVERT: AJ 141 MET cc_start: 0.7852 (ptp) cc_final: 0.7595 (ptp) REVERT: AN 91 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8375 (mm) REVERT: AO 96 MET cc_start: 0.8172 (tmm) cc_final: 0.7919 (tmm) REVERT: AU 53 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7629 (tm-30) REVERT: AU 145 ASP cc_start: 0.8477 (m-30) cc_final: 0.7983 (m-30) REVERT: AV 15 GLN cc_start: 0.8148 (mp10) cc_final: 0.7869 (mp10) REVERT: AW 88 TYR cc_start: 0.8085 (m-80) cc_final: 0.7881 (m-80) REVERT: AW 144 ASP cc_start: 0.7665 (p0) cc_final: 0.7416 (p0) REVERT: AW 160 MET cc_start: 0.8682 (tpp) cc_final: 0.8465 (mmt) REVERT: BB 24 ASN cc_start: 0.8223 (t0) cc_final: 0.7747 (t0) REVERT: BB 46 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5915 (mmt) REVERT: BB 53 VAL cc_start: 0.8285 (m) cc_final: 0.8050 (t) REVERT: BH 32 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8294 (p0) REVERT: BH 164 THR cc_start: 0.8607 (p) cc_final: 0.8321 (t) REVERT: BH 174 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.5717 (pp20) outliers start: 102 outliers final: 13 residues processed: 945 average time/residue: 0.7968 time to fit residues: 893.6685 Evaluate side-chains 609 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 590 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 128 GLN Chi-restraints excluded: chain AC residue 96 VAL Chi-restraints excluded: chain AC residue 124 GLU Chi-restraints excluded: chain AE residue 14 GLN Chi-restraints excluded: chain AE residue 149 THR Chi-restraints excluded: chain AJ residue 9 VAL Chi-restraints excluded: chain AJ residue 66 VAL Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 144 ASP Chi-restraints excluded: chain AN residue 91 LEU Chi-restraints excluded: chain AU residue 30 VAL Chi-restraints excluded: chain AV residue 112 LEU Chi-restraints excluded: chain BB residue 46 MET Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BH residue 32 ASN Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 53 GLN AA 128 GLN AB 131 GLN AD 71 ASN AE 10 GLN AE 79 ASN AE 117 ASN AE 120 ASN AK 22 ASN AK 72 ASN AO 10 ASN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 10 ASN AX 2 GLN BB 40 GLN BE 27 GLN BE 30 GLN ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 213 ASN BE 444 GLN BE 451 ASN BI 97 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050814 restraints weight = 119420.373| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.53 r_work: 0.2920 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37841 Z= 0.136 Angle : 0.635 13.079 51257 Z= 0.316 Chirality : 0.037 0.168 5740 Planarity : 0.004 0.055 6586 Dihedral : 8.752 86.807 6424 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.58 % Favored : 98.38 % Rotamer: Outliers : 3.24 % Allowed : 18.30 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.88 (0.11), residues: 4683 helix: -0.19 (0.08), residues: 3623 sheet: -0.62 (0.84), residues: 38 loop : -1.59 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGBE 33 TYR 0.020 0.001 TYRBE 597 PHE 0.014 0.001 PHEBE 424 TRP 0.018 0.001 TRPBE 158 HIS 0.003 0.001 HISAE 62 Details of bonding type rmsd covalent geometry : bond 0.00297 (37817) covalent geometry : angle 0.63513 (51257) hydrogen bonds : bond 0.04090 ( 2490) hydrogen bonds : angle 4.43105 ( 7446) Misc. bond : bond 0.00033 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 655 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9421 (p0) cc_final: 0.9179 (p0) REVERT: AA 105 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7906 (mm-30) REVERT: AA 128 GLN cc_start: 0.8211 (tp40) cc_final: 0.7970 (tp40) REVERT: AB 10 ASN cc_start: 0.8404 (t0) cc_final: 0.8148 (t0) REVERT: AB 13 ASP cc_start: 0.8923 (t70) cc_final: 0.8597 (t0) REVERT: AB 28 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8797 (mmmm) REVERT: AB 39 ARG cc_start: 0.8144 (tmm-80) cc_final: 0.7896 (tmm-80) REVERT: AB 54 GLU cc_start: 0.9038 (tp30) cc_final: 0.8753 (tp30) REVERT: AB 67 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7545 (mtm110) REVERT: AB 100 ASP cc_start: 0.7635 (t70) cc_final: 0.7101 (t0) REVERT: AB 113 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8003 (tptm) REVERT: AB 117 ASN cc_start: 0.8589 (m-40) cc_final: 0.8219 (m-40) REVERT: AB 128 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: AB 154 ASP cc_start: 0.8541 (m-30) cc_final: 0.8334 (m-30) REVERT: AC 24 ASP cc_start: 0.8379 (m-30) cc_final: 0.7738 (t0) REVERT: AC 27 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8832 (pptt) REVERT: AC 52 LYS cc_start: 0.8890 (tptp) cc_final: 0.8674 (tppt) REVERT: AC 53 GLN cc_start: 0.8324 (mp10) cc_final: 0.8095 (mp10) REVERT: AC 56 ASP cc_start: 0.8655 (m-30) cc_final: 0.8413 (m-30) REVERT: AC 60 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8443 (tm-30) REVERT: AC 61 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8484 (ttmm) REVERT: AC 73 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.6283 (m-10) REVERT: AC 124 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: AD 2 GLN cc_start: 0.8272 (pm20) cc_final: 0.7855 (pm20) REVERT: AD 37 ARG cc_start: 0.8804 (mtt90) cc_final: 0.8453 (mtp85) REVERT: AD 39 ARG cc_start: 0.9059 (mmm160) cc_final: 0.8857 (mmm160) REVERT: AD 43 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8736 (m) REVERT: AD 47 ASN cc_start: 0.7926 (m110) cc_final: 0.7693 (m110) REVERT: AD 113 LYS cc_start: 0.7804 (tttp) cc_final: 0.7475 (tttm) REVERT: AD 117 ASN cc_start: 0.9095 (m110) cc_final: 0.8795 (m-40) REVERT: AD 128 GLN cc_start: 0.8190 (tp40) cc_final: 0.7794 (mm110) REVERT: AD 131 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7974 (tm-30) REVERT: AD 135 GLU cc_start: 0.8561 (mp0) cc_final: 0.8265 (mp0) REVERT: AE 12 ASP cc_start: 0.8066 (t70) cc_final: 0.7831 (t0) REVERT: AE 14 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8683 (mp10) REVERT: AE 46 ASN cc_start: 0.6995 (t0) cc_final: 0.6786 (t0) REVERT: AE 53 GLN cc_start: 0.8394 (tp-100) cc_final: 0.8003 (tp-100) REVERT: AE 60 LYS cc_start: 0.8992 (ttpp) cc_final: 0.8589 (tptp) REVERT: AE 61 LYS cc_start: 0.9026 (tttp) cc_final: 0.8745 (tttt) REVERT: AF 15 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7641 (mp-120) REVERT: AF 17 LYS cc_start: 0.7493 (mtmp) cc_final: 0.7106 (mtmm) REVERT: AF 28 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8711 (mtmt) REVERT: AF 71 ASN cc_start: 0.8306 (t0) cc_final: 0.7970 (t0) REVERT: AF 72 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.6638 (tmm) REVERT: AF 86 ASP cc_start: 0.8094 (t70) cc_final: 0.7864 (t0) REVERT: AF 100 ASP cc_start: 0.7762 (t70) cc_final: 0.7089 (t0) REVERT: AF 105 ASP cc_start: 0.8975 (t0) cc_final: 0.8687 (m-30) REVERT: AF 131 GLN cc_start: 0.7555 (mm110) cc_final: 0.7337 (mm-40) REVERT: AF 157 CYS cc_start: 0.7502 (m) cc_final: 0.7295 (m) REVERT: AH 49 THR cc_start: 0.9670 (OUTLIER) cc_final: 0.9443 (t) REVERT: AH 61 LYS cc_start: 0.9527 (mtpp) cc_final: 0.9312 (mtmm) REVERT: AH 100 ASP cc_start: 0.8674 (t0) cc_final: 0.8243 (t70) REVERT: AI 2 GLN cc_start: 0.8736 (mt0) cc_final: 0.8509 (mt0) REVERT: AJ 66 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8599 (m) REVERT: AJ 140 LEU cc_start: 0.8554 (mt) cc_final: 0.8344 (mp) REVERT: AK 22 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8450 (t0) REVERT: AK 137 MET cc_start: 0.7879 (mtp) cc_final: 0.7598 (mtp) REVERT: AL 1 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8494 (ptt) REVERT: AL 54 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: AL 135 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8313 (mm-30) REVERT: AN 44 THR cc_start: 0.8922 (m) cc_final: 0.8588 (p) REVERT: AN 133 MET cc_start: 0.8304 (mtm) cc_final: 0.8055 (mtp) REVERT: AO 10 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8088 (t0) REVERT: AO 24 MET cc_start: 0.8805 (mpp) cc_final: 0.8569 (mpp) REVERT: AO 96 MET cc_start: 0.9216 (tmm) cc_final: 0.9008 (tmm) REVERT: AQ 149 MET cc_start: 0.9406 (mmm) cc_final: 0.8966 (tpp) REVERT: AR 24 ASP cc_start: 0.9111 (t0) cc_final: 0.8881 (t0) REVERT: AS 26 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9120 (ttmt) REVERT: AS 106 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8622 (mm-30) REVERT: AU 27 LYS cc_start: 0.9024 (ptmm) cc_final: 0.8729 (ptpp) REVERT: AU 53 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7872 (tm-30) REVERT: AU 100 ASP cc_start: 0.8398 (t0) cc_final: 0.7942 (t0) REVERT: AU 144 ASP cc_start: 0.7904 (p0) cc_final: 0.7556 (p0) REVERT: AU 145 ASP cc_start: 0.8706 (m-30) cc_final: 0.8456 (m-30) REVERT: AV 15 GLN cc_start: 0.8605 (mp10) cc_final: 0.8144 (mp10) REVERT: AV 26 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.9001 (mmmm) REVERT: AV 35 GLU cc_start: 0.8640 (tp30) cc_final: 0.8092 (tp30) REVERT: AV 39 ARG cc_start: 0.9253 (ptp-110) cc_final: 0.8822 (ptp-110) REVERT: AV 106 GLU cc_start: 0.8994 (tt0) cc_final: 0.8606 (tt0) REVERT: AV 147 LYS cc_start: 0.9057 (tppp) cc_final: 0.8463 (tppt) REVERT: AW 61 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8694 (ttmm) REVERT: AW 100 ASP cc_start: 0.7794 (t0) cc_final: 0.7313 (t0) REVERT: AW 160 MET cc_start: 0.8708 (tpp) cc_final: 0.8364 (mmt) REVERT: AX 15 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8747 (pm20) REVERT: AZ 54 GLU cc_start: 0.8856 (mp0) cc_final: 0.8630 (mp0) REVERT: AZ 147 LYS cc_start: 0.9428 (tppp) cc_final: 0.9067 (ttpp) REVERT: BB 24 ASN cc_start: 0.9010 (t0) cc_final: 0.8208 (t0) REVERT: BB 46 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6716 (mpt) REVERT: BC 54 GLU cc_start: 0.8695 (pt0) cc_final: 0.8245 (pm20) REVERT: BE 384 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8340 (tp-100) REVERT: BG 202 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8849 (ttm-80) REVERT: BH 32 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8617 (p0) REVERT: BH 65 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7992 (tm-30) REVERT: BH 70 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8259 (tm-30) REVERT: BH 74 MET cc_start: 0.7944 (mtp) cc_final: 0.7710 (mtp) REVERT: BH 174 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6909 (pp20) REVERT: BI 116 GLN cc_start: 0.8326 (mm110) cc_final: 0.8096 (mm110) outliers start: 123 outliers final: 25 residues processed: 736 average time/residue: 0.7721 time to fit residues: 675.3263 Evaluate side-chains 623 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 576 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 67 ARG Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 113 LYS Chi-restraints excluded: chain AB residue 128 GLN Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AC residue 102 THR Chi-restraints excluded: chain AC residue 124 GLU Chi-restraints excluded: chain AD residue 43 VAL Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AE residue 14 GLN Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AF residue 72 MET Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 49 THR Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 102 THR Chi-restraints excluded: chain AJ residue 66 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 22 ASN Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 160 MET Chi-restraints excluded: chain AL residue 1 MET Chi-restraints excluded: chain AL residue 54 GLU Chi-restraints excluded: chain AN residue 140 LEU Chi-restraints excluded: chain AO residue 10 ASN Chi-restraints excluded: chain AS residue 26 LYS Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AV residue 26 LYS Chi-restraints excluded: chain AX residue 15 GLN Chi-restraints excluded: chain AX residue 27 LEU Chi-restraints excluded: chain BB residue 46 MET Chi-restraints excluded: chain BC residue 51 VAL Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 384 GLN Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 32 ASN Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 174 GLU Chi-restraints excluded: chain BI residue 97 ASN Chi-restraints excluded: chain BI residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 8 optimal weight: 8.9990 chunk 281 optimal weight: 0.9980 chunk 411 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 440 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 435 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 424 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AE 57 GLN AE 77 GLN AE 120 ASN AF 2 GLN ** AF 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 128 GLN AK 22 ASN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 131 GLN AV 2 GLN BC 13 GLN BE 31 GLN ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 451 ASN ** BH 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.061778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048125 restraints weight = 120147.753| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.67 r_work: 0.2826 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37841 Z= 0.183 Angle : 0.625 12.720 51257 Z= 0.306 Chirality : 0.038 0.166 5740 Planarity : 0.004 0.056 6586 Dihedral : 8.172 87.657 6413 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.96 % Favored : 98.01 % Rotamer: Outliers : 3.30 % Allowed : 19.41 % Favored : 77.29 % 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: 0.61 (0.12), residues: 4683 helix: 0.92 (0.08), residues: 3613 sheet: -0.50 (0.81), residues: 38 loop : -1.21 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGAD 67 TYR 0.025 0.002 TYRBE 597 PHE 0.014 0.001 PHEBE 76 TRP 0.015 0.001 TRPBE 158 HIS 0.003 0.001 HISBE 349 Details of bonding type rmsd covalent geometry : bond 0.00414 (37817) covalent geometry : angle 0.62457 (51257) hydrogen bonds : bond 0.03728 ( 2490) hydrogen bonds : angle 4.08700 ( 7446) Misc. bond : bond 0.00079 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 611 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9452 (p0) cc_final: 0.9193 (p0) REVERT: AA 128 GLN cc_start: 0.8174 (tp40) cc_final: 0.7892 (tp-100) REVERT: AA 138 SER cc_start: 0.8854 (m) cc_final: 0.8602 (p) REVERT: AA 145 ASP cc_start: 0.8060 (m-30) cc_final: 0.7652 (m-30) REVERT: AB 10 ASN cc_start: 0.8442 (t0) cc_final: 0.8204 (t0) REVERT: AB 13 ASP cc_start: 0.8955 (t70) cc_final: 0.8699 (t0) REVERT: AB 28 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8808 (mmmm) REVERT: AB 54 GLU cc_start: 0.9125 (tp30) cc_final: 0.8794 (tp30) REVERT: AB 67 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7478 (mtm110) REVERT: AB 96 MET cc_start: 0.8564 (ttp) cc_final: 0.8320 (ttm) REVERT: AB 100 ASP cc_start: 0.7518 (t70) cc_final: 0.7030 (t0) REVERT: AB 128 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: AC 24 ASP cc_start: 0.8345 (m-30) cc_final: 0.7883 (t0) REVERT: AC 27 LYS cc_start: 0.9069 (ttpt) cc_final: 0.8791 (pptt) REVERT: AC 53 GLN cc_start: 0.8185 (mp10) cc_final: 0.7888 (mp10) REVERT: AC 56 ASP cc_start: 0.8572 (m-30) cc_final: 0.8255 (m-30) REVERT: AC 60 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8467 (tm-30) REVERT: AC 61 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8446 (ttmt) REVERT: AC 73 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: AC 100 ASP cc_start: 0.7609 (t70) cc_final: 0.7337 (t70) REVERT: AC 124 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: AC 159 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8707 (tppp) REVERT: AD 2 GLN cc_start: 0.8208 (pm20) cc_final: 0.7740 (pm20) REVERT: AD 17 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8612 (ptpp) REVERT: AD 39 ARG cc_start: 0.9070 (mmm160) cc_final: 0.8765 (mmm160) REVERT: AD 100 ASP cc_start: 0.7404 (t70) cc_final: 0.7202 (t70) REVERT: AD 105 ASP cc_start: 0.8793 (m-30) cc_final: 0.8536 (m-30) REVERT: AD 113 LYS cc_start: 0.8010 (tttp) cc_final: 0.7663 (tttm) REVERT: AD 117 ASN cc_start: 0.8949 (m110) cc_final: 0.8688 (m-40) REVERT: AD 128 GLN cc_start: 0.8126 (tp40) cc_final: 0.7830 (mm110) REVERT: AD 131 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7721 (tm-30) REVERT: AD 135 GLU cc_start: 0.8619 (mp0) cc_final: 0.7945 (mp0) REVERT: AD 148 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8558 (tm-30) REVERT: AD 154 ASP cc_start: 0.8998 (m-30) cc_final: 0.8735 (m-30) REVERT: AE 14 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8709 (mp10) REVERT: AE 22 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8040 (pt0) REVERT: AE 53 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8342 (tp-100) REVERT: AE 61 LYS cc_start: 0.9086 (tttp) cc_final: 0.8805 (tttt) REVERT: AE 83 ARG cc_start: 0.8038 (tmm-80) cc_final: 0.7729 (tmm-80) REVERT: AF 2 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6265 (tm-30) REVERT: AF 17 LYS cc_start: 0.7472 (mtmp) cc_final: 0.7070 (mtmm) REVERT: AF 20 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8584 (p0) REVERT: AF 71 ASN cc_start: 0.8397 (t0) cc_final: 0.7891 (t0) REVERT: AF 100 ASP cc_start: 0.7739 (t70) cc_final: 0.7114 (t0) REVERT: AF 105 ASP cc_start: 0.8928 (t0) cc_final: 0.8709 (m-30) REVERT: AF 114 GLU cc_start: 0.8544 (tt0) cc_final: 0.7705 (tt0) REVERT: AH 61 LYS cc_start: 0.9604 (mtpp) cc_final: 0.9329 (mtmm) REVERT: AH 100 ASP cc_start: 0.8821 (t0) cc_final: 0.8432 (t70) REVERT: AI 2 GLN cc_start: 0.8779 (mt0) cc_final: 0.8519 (mt0) REVERT: AJ 66 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8914 (m) REVERT: AK 22 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8515 (t0) REVERT: AK 24 MET cc_start: 0.8619 (mmt) cc_final: 0.8292 (mmt) REVERT: AL 54 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: AL 135 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8503 (mm-30) REVERT: AL 144 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8424 (p0) REVERT: AN 44 THR cc_start: 0.9080 (m) cc_final: 0.8712 (p) REVERT: AN 115 MET cc_start: 0.9091 (tmm) cc_final: 0.8850 (tmm) REVERT: AN 141 MET cc_start: 0.8454 (ttm) cc_final: 0.8119 (ttp) REVERT: AO 96 MET cc_start: 0.9270 (tmm) cc_final: 0.9045 (tmm) REVERT: AO 148 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8359 (tm-30) REVERT: AQ 149 MET cc_start: 0.9424 (mmm) cc_final: 0.9120 (tpp) REVERT: AR 24 ASP cc_start: 0.9116 (t0) cc_final: 0.8892 (t0) REVERT: AS 106 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8669 (mm-30) REVERT: AU 24 ASP cc_start: 0.8648 (m-30) cc_final: 0.8366 (m-30) REVERT: AU 27 LYS cc_start: 0.9076 (ptmm) cc_final: 0.8697 (ptpp) REVERT: AU 53 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7861 (tm-30) REVERT: AU 100 ASP cc_start: 0.8336 (t0) cc_final: 0.7926 (t0) REVERT: AU 144 ASP cc_start: 0.8027 (p0) cc_final: 0.7716 (p0) REVERT: AU 145 ASP cc_start: 0.8714 (m-30) cc_final: 0.8489 (m-30) REVERT: AV 1 MET cc_start: 0.8075 (pmm) cc_final: 0.7613 (ppp) REVERT: AV 15 GLN cc_start: 0.8685 (mp10) cc_final: 0.8160 (mp10) REVERT: AV 26 LYS cc_start: 0.9237 (mmmm) cc_final: 0.9035 (mmmm) REVERT: AV 35 GLU cc_start: 0.8728 (tp30) cc_final: 0.8212 (tp30) REVERT: AV 39 ARG cc_start: 0.9278 (ptp-110) cc_final: 0.8901 (ptp-110) REVERT: AV 106 GLU cc_start: 0.9017 (tt0) cc_final: 0.8661 (tt0) REVERT: AV 147 LYS cc_start: 0.9063 (tppp) cc_final: 0.8476 (tppt) REVERT: AW 66 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8554 (m) REVERT: AW 100 ASP cc_start: 0.8258 (t0) cc_final: 0.7501 (t0) REVERT: AX 1 MET cc_start: 0.8201 (ptm) cc_final: 0.7950 (ptm) REVERT: AX 54 GLU cc_start: 0.9183 (tt0) cc_final: 0.8678 (tm-30) REVERT: AZ 15 GLN cc_start: 0.9048 (mp10) cc_final: 0.8356 (mp10) REVERT: AZ 54 GLU cc_start: 0.8974 (mp0) cc_final: 0.8683 (mp0) REVERT: AZ 67 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8395 (ptp-110) REVERT: AZ 147 LYS cc_start: 0.9462 (tppp) cc_final: 0.9125 (ttpp) REVERT: BB 24 ASN cc_start: 0.9081 (t0) cc_final: 0.8366 (t0) REVERT: BB 44 MET cc_start: 0.9145 (ptm) cc_final: 0.8905 (ptm) REVERT: BB 59 ARG cc_start: 0.8447 (mmm160) cc_final: 0.8138 (mmm160) REVERT: BC 3 MET cc_start: 0.8839 (mtp) cc_final: 0.8587 (mtp) REVERT: BC 21 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7662 (mm-30) REVERT: BC 54 GLU cc_start: 0.8683 (pt0) cc_final: 0.8168 (pm20) REVERT: BH 35 ASP cc_start: 0.9342 (m-30) cc_final: 0.9131 (m-30) REVERT: BH 65 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8053 (tm-30) REVERT: BH 70 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8318 (tm-30) REVERT: BH 74 MET cc_start: 0.8066 (mtp) cc_final: 0.7668 (mtp) REVERT: BH 174 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7310 (pp20) REVERT: BI 113 MET cc_start: 0.8743 (mtm) cc_final: 0.8186 (mtp) outliers start: 125 outliers final: 45 residues processed: 683 average time/residue: 0.7553 time to fit residues: 614.9505 Evaluate side-chains 624 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 565 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 49 THR Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 67 ARG Chi-restraints excluded: chain AB residue 118 SER Chi-restraints excluded: chain AB residue 128 GLN Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AC residue 102 THR Chi-restraints excluded: chain AC residue 124 GLU Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AE residue 14 GLN Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AF residue 2 GLN Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 133 ILE Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 161 SER Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AJ residue 66 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 22 ASN Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 160 MET Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 54 GLU Chi-restraints excluded: chain AL residue 144 ASP Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AS residue 26 LYS Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 139 SER Chi-restraints excluded: chain AS residue 141 VAL Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AZ residue 67 ARG Chi-restraints excluded: chain BB residue 1 MET Chi-restraints excluded: chain BB residue 7 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BC residue 51 VAL Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 212 ASN Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 384 GLN Chi-restraints excluded: chain BE residue 515 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Chi-restraints excluded: chain BI residue 97 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 393 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN ** AB 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN ** AF 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 128 GLN AK 22 ASN AO 10 ASN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 2 GLN ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047159 restraints weight = 120026.067| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.58 r_work: 0.2803 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37841 Z= 0.196 Angle : 0.637 12.797 51257 Z= 0.310 Chirality : 0.039 0.180 5740 Planarity : 0.004 0.040 6586 Dihedral : 7.980 85.684 6408 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.96 % Favored : 98.01 % Rotamer: Outliers : 3.35 % Allowed : 19.83 % Favored : 76.82 % 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 (0.12), residues: 4683 helix: 1.32 (0.08), residues: 3618 sheet: 0.79 (1.02), residues: 26 loop : -0.96 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAD 67 TYR 0.026 0.002 TYRBE 597 PHE 0.015 0.001 PHEBE 424 TRP 0.015 0.001 TRPBE 158 HIS 0.003 0.001 HISBE 349 Details of bonding type rmsd covalent geometry : bond 0.00446 (37817) covalent geometry : angle 0.63727 (51257) hydrogen bonds : bond 0.03584 ( 2490) hydrogen bonds : angle 4.06486 ( 7446) Misc. bond : bond 0.00097 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 606 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9451 (p0) cc_final: 0.9159 (p0) REVERT: AA 128 GLN cc_start: 0.8155 (tp40) cc_final: 0.7883 (tp-100) REVERT: AA 138 SER cc_start: 0.8884 (m) cc_final: 0.8677 (p) REVERT: AB 13 ASP cc_start: 0.9006 (t70) cc_final: 0.8793 (t0) REVERT: AB 28 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8829 (mmmm) REVERT: AB 35 GLU cc_start: 0.8522 (mp0) cc_final: 0.8062 (mp0) REVERT: AB 54 GLU cc_start: 0.9113 (tp30) cc_final: 0.8834 (tp30) REVERT: AB 58 LYS cc_start: 0.8885 (ptmm) cc_final: 0.8579 (ptmm) REVERT: AB 67 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7534 (mtm110) REVERT: AB 83 ARG cc_start: 0.7339 (ttp80) cc_final: 0.7073 (ttp-170) REVERT: AB 100 ASP cc_start: 0.7530 (t70) cc_final: 0.7065 (t0) REVERT: AC 24 ASP cc_start: 0.8361 (m-30) cc_final: 0.7948 (t0) REVERT: AC 27 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8853 (pptt) REVERT: AC 53 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: AC 60 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8492 (tm-30) REVERT: AC 61 LYS cc_start: 0.8761 (ttmm) cc_final: 0.8467 (ttmt) REVERT: AC 100 ASP cc_start: 0.7685 (t70) cc_final: 0.7410 (t70) REVERT: AC 141 MET cc_start: 0.6813 (ptm) cc_final: 0.6244 (pp-130) REVERT: AC 159 LYS cc_start: 0.9033 (ttmm) cc_final: 0.8669 (tppp) REVERT: AD 2 GLN cc_start: 0.8188 (pm20) cc_final: 0.7643 (pm20) REVERT: AD 17 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8517 (ptpp) REVERT: AD 47 ASN cc_start: 0.7227 (t0) cc_final: 0.6814 (t0) REVERT: AD 105 ASP cc_start: 0.8847 (m-30) cc_final: 0.8546 (m-30) REVERT: AD 113 LYS cc_start: 0.7981 (tttp) cc_final: 0.7726 (tttm) REVERT: AD 117 ASN cc_start: 0.8885 (m110) cc_final: 0.8678 (m110) REVERT: AD 128 GLN cc_start: 0.8197 (tp40) cc_final: 0.7946 (mm110) REVERT: AD 131 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7657 (tm-30) REVERT: AD 135 GLU cc_start: 0.8557 (mp0) cc_final: 0.7730 (mp0) REVERT: AD 154 ASP cc_start: 0.8970 (m-30) cc_final: 0.8695 (m-30) REVERT: AE 49 LYS cc_start: 0.8765 (tptp) cc_final: 0.8356 (tptp) REVERT: AE 60 LYS cc_start: 0.8787 (tmmm) cc_final: 0.8579 (tptp) REVERT: AE 61 LYS cc_start: 0.9158 (tttp) cc_final: 0.8821 (tttt) REVERT: AE 83 ARG cc_start: 0.8063 (tmm-80) cc_final: 0.7772 (tmm-80) REVERT: AE 113 LYS cc_start: 0.7808 (tppp) cc_final: 0.7547 (mmmm) REVERT: AE 115 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7891 (tmm) REVERT: AF 71 ASN cc_start: 0.8466 (t0) cc_final: 0.8168 (t0) REVERT: AF 100 ASP cc_start: 0.7961 (t70) cc_final: 0.7286 (t0) REVERT: AF 114 GLU cc_start: 0.8535 (tt0) cc_final: 0.8211 (tt0) REVERT: AH 61 LYS cc_start: 0.9635 (mtpp) cc_final: 0.9362 (mtmm) REVERT: AH 100 ASP cc_start: 0.8816 (t0) cc_final: 0.8305 (t0) REVERT: AI 36 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9094 (tp) REVERT: AL 54 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: AN 44 THR cc_start: 0.9116 (m) cc_final: 0.8745 (p) REVERT: AN 141 MET cc_start: 0.8422 (ttm) cc_final: 0.8120 (ttp) REVERT: AO 24 MET cc_start: 0.8878 (mpp) cc_final: 0.8652 (mpp) REVERT: AP 98 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.9338 (m) REVERT: AQ 149 MET cc_start: 0.9400 (mmm) cc_final: 0.9077 (tpp) REVERT: AS 106 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8710 (mm-30) REVERT: AS 131 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8525 (mm110) REVERT: AU 6 LYS cc_start: 0.9058 (mttp) cc_final: 0.8843 (mmtp) REVERT: AU 24 ASP cc_start: 0.8701 (m-30) cc_final: 0.8419 (m-30) REVERT: AU 27 LYS cc_start: 0.9113 (ptmm) cc_final: 0.8766 (ptpp) REVERT: AU 100 ASP cc_start: 0.8244 (t0) cc_final: 0.7845 (t0) REVERT: AU 144 ASP cc_start: 0.7960 (p0) cc_final: 0.7627 (p0) REVERT: AU 145 ASP cc_start: 0.8763 (m-30) cc_final: 0.8546 (m-30) REVERT: AV 1 MET cc_start: 0.8010 (pmm) cc_final: 0.7586 (ppp) REVERT: AV 15 GLN cc_start: 0.8728 (mp10) cc_final: 0.8336 (mp10) REVERT: AV 35 GLU cc_start: 0.8764 (tp30) cc_final: 0.8263 (tp30) REVERT: AV 39 ARG cc_start: 0.9295 (ptp-110) cc_final: 0.9023 (ptp-110) REVERT: AV 106 GLU cc_start: 0.9007 (tt0) cc_final: 0.8637 (tt0) REVERT: AV 147 LYS cc_start: 0.9082 (tppp) cc_final: 0.8489 (tppt) REVERT: AW 66 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8591 (m) REVERT: AW 100 ASP cc_start: 0.8355 (t0) cc_final: 0.7535 (t0) REVERT: AW 141 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7184 (ppp) REVERT: AX 54 GLU cc_start: 0.9144 (tt0) cc_final: 0.8699 (tm-30) REVERT: AX 148 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8884 (tm-30) REVERT: AY 27 LYS cc_start: 0.8988 (tptt) cc_final: 0.8710 (mmmt) REVERT: AY 160 MET cc_start: 0.9442 (tpp) cc_final: 0.9164 (mmt) REVERT: AZ 35 GLU cc_start: 0.8411 (mp0) cc_final: 0.8117 (mp0) REVERT: AZ 147 LYS cc_start: 0.9488 (tppp) cc_final: 0.9165 (ttpp) REVERT: BB 24 ASN cc_start: 0.9129 (t0) cc_final: 0.8471 (t0) REVERT: BB 59 ARG cc_start: 0.8389 (mmm160) cc_final: 0.8119 (mmm160) REVERT: BC 3 MET cc_start: 0.8896 (mtp) cc_final: 0.8639 (mtp) REVERT: BC 21 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7726 (mm-30) REVERT: BC 54 GLU cc_start: 0.8568 (pt0) cc_final: 0.8010 (pm20) REVERT: BE 277 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.9116 (pm20) REVERT: BH 34 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: BH 35 ASP cc_start: 0.9209 (m-30) cc_final: 0.8601 (m-30) REVERT: BH 65 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8066 (tm-30) REVERT: BH 70 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8226 (tm-30) REVERT: BH 74 MET cc_start: 0.8193 (mtm) cc_final: 0.7718 (mtp) REVERT: BH 174 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6984 (pp20) REVERT: BI 112 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8250 (mm-30) outliers start: 127 outliers final: 57 residues processed: 688 average time/residue: 0.7585 time to fit residues: 621.4509 Evaluate side-chains 643 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 574 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 67 ARG Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 118 SER Chi-restraints excluded: chain AB residue 128 GLN Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 91 LEU Chi-restraints excluded: chain AC residue 102 THR Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AE residue 85 TYR Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AE residue 145 ASP Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 133 ILE Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AF residue 161 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 102 THR Chi-restraints excluded: chain AI residue 36 LEU Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 160 MET Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 54 GLU Chi-restraints excluded: chain AL residue 161 SER Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AP residue 98 SER Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 139 SER Chi-restraints excluded: chain AS residue 141 VAL Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 140 LEU Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AW residue 141 MET Chi-restraints excluded: chain AZ residue 66 THR Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 7 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BC residue 51 VAL Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 277 GLU Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 384 GLN Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 34 GLU Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Chi-restraints excluded: chain BI residue 112 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 199 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 378 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 117 ASN AD 15 GLN AE 120 ASN ** AF 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 128 GLN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 2 GLN BC 13 GLN BE 27 GLN ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.046561 restraints weight = 119337.519| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.56 r_work: 0.2779 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 37841 Z= 0.222 Angle : 0.659 12.609 51257 Z= 0.321 Chirality : 0.040 0.171 5740 Planarity : 0.004 0.051 6586 Dihedral : 7.856 84.358 6401 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Rotamer: Outliers : 3.43 % Allowed : 20.97 % Favored : 75.61 % 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: 1.44 (0.12), residues: 4683 helix: 1.51 (0.09), residues: 3598 sheet: 1.12 (1.06), residues: 26 loop : -0.89 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGAD 39 TYR 0.027 0.002 TYRBE 597 PHE 0.015 0.001 PHEBE 424 TRP 0.014 0.001 TRPBE 158 HIS 0.003 0.001 HISBE 349 Details of bonding type rmsd covalent geometry : bond 0.00505 (37817) covalent geometry : angle 0.65854 (51257) hydrogen bonds : bond 0.03636 ( 2490) hydrogen bonds : angle 4.10521 ( 7446) Misc. bond : bond 0.00108 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 602 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9441 (p0) cc_final: 0.9165 (p0) REVERT: AA 128 GLN cc_start: 0.8118 (tp40) cc_final: 0.7863 (tp-100) REVERT: AB 28 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8888 (mmmm) REVERT: AB 35 GLU cc_start: 0.8574 (mp0) cc_final: 0.8255 (mp0) REVERT: AB 54 GLU cc_start: 0.9204 (tp30) cc_final: 0.8932 (tp30) REVERT: AB 67 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7462 (mtm110) REVERT: AB 83 ARG cc_start: 0.7325 (ttp80) cc_final: 0.7030 (ttp-170) REVERT: AB 100 ASP cc_start: 0.7515 (t70) cc_final: 0.7069 (t0) REVERT: AC 24 ASP cc_start: 0.8357 (m-30) cc_final: 0.7966 (t0) REVERT: AC 27 LYS cc_start: 0.9139 (ttpt) cc_final: 0.8900 (pptt) REVERT: AC 53 GLN cc_start: 0.7778 (mp10) cc_final: 0.7526 (mp10) REVERT: AC 60 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8466 (tm-30) REVERT: AC 61 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8551 (ttmt) REVERT: AC 100 ASP cc_start: 0.7720 (t70) cc_final: 0.7446 (t70) REVERT: AC 159 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8635 (tppp) REVERT: AD 2 GLN cc_start: 0.8299 (pm20) cc_final: 0.7758 (pm20) REVERT: AD 17 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8560 (ptpp) REVERT: AD 58 LYS cc_start: 0.8860 (ptpp) cc_final: 0.8613 (ptpp) REVERT: AD 64 ASP cc_start: 0.8649 (m-30) cc_final: 0.8428 (m-30) REVERT: AD 84 ASP cc_start: 0.8763 (m-30) cc_final: 0.8419 (m-30) REVERT: AD 105 ASP cc_start: 0.8908 (m-30) cc_final: 0.8631 (m-30) REVERT: AD 113 LYS cc_start: 0.8006 (tttp) cc_final: 0.7785 (tttm) REVERT: AD 128 GLN cc_start: 0.8264 (tp40) cc_final: 0.8001 (mm110) REVERT: AD 131 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7798 (tm-30) REVERT: AD 135 GLU cc_start: 0.8641 (mp0) cc_final: 0.8151 (mp0) REVERT: AE 22 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8151 (pt0) REVERT: AE 41 GLU cc_start: 0.8220 (mp0) cc_final: 0.7850 (mp0) REVERT: AE 49 LYS cc_start: 0.8802 (tptp) cc_final: 0.8526 (tptp) REVERT: AE 60 LYS cc_start: 0.8813 (tmmm) cc_final: 0.8559 (tptp) REVERT: AE 61 LYS cc_start: 0.9257 (tttp) cc_final: 0.9031 (tttt) REVERT: AE 113 LYS cc_start: 0.7844 (tppp) cc_final: 0.7580 (mmmm) REVERT: AE 115 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7928 (tmm) REVERT: AF 17 LYS cc_start: 0.7251 (mtmm) cc_final: 0.6899 (mtmm) REVERT: AF 71 ASN cc_start: 0.8424 (t0) cc_final: 0.7915 (t0) REVERT: AF 100 ASP cc_start: 0.7932 (t70) cc_final: 0.7285 (t0) REVERT: AF 105 ASP cc_start: 0.8994 (t0) cc_final: 0.8722 (m-30) REVERT: AH 61 LYS cc_start: 0.9658 (mtpp) cc_final: 0.9367 (mtmm) REVERT: AH 100 ASP cc_start: 0.9040 (t0) cc_final: 0.8553 (t0) REVERT: AI 36 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9126 (tp) REVERT: AJ 27 LYS cc_start: 0.9027 (tptt) cc_final: 0.8744 (ttpp) REVERT: AL 54 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8693 (mp0) REVERT: AN 44 THR cc_start: 0.9201 (m) cc_final: 0.8791 (p) REVERT: AN 141 MET cc_start: 0.8482 (ttm) cc_final: 0.8194 (ttp) REVERT: AO 96 MET cc_start: 0.9415 (tmm) cc_final: 0.9197 (tmm) REVERT: AQ 149 MET cc_start: 0.9521 (mmm) cc_final: 0.9197 (tpp) REVERT: AU 24 ASP cc_start: 0.8849 (m-30) cc_final: 0.8575 (m-30) REVERT: AU 27 LYS cc_start: 0.9158 (ptmm) cc_final: 0.8808 (ptpp) REVERT: AU 144 ASP cc_start: 0.8101 (p0) cc_final: 0.7803 (p0) REVERT: AU 145 ASP cc_start: 0.8831 (m-30) cc_final: 0.8630 (m-30) REVERT: AV 1 MET cc_start: 0.8043 (pmm) cc_final: 0.7546 (ppp) REVERT: AV 15 GLN cc_start: 0.8697 (mp10) cc_final: 0.8236 (mp10) REVERT: AV 35 GLU cc_start: 0.8939 (tp30) cc_final: 0.8431 (tp30) REVERT: AV 39 ARG cc_start: 0.9397 (ptp-110) cc_final: 0.9143 (ptp-110) REVERT: AV 106 GLU cc_start: 0.9104 (tt0) cc_final: 0.8717 (tt0) REVERT: AW 66 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8580 (m) REVERT: AW 100 ASP cc_start: 0.8548 (t0) cc_final: 0.7677 (t0) REVERT: AX 54 GLU cc_start: 0.9285 (tt0) cc_final: 0.8872 (tm-30) REVERT: AY 160 MET cc_start: 0.9466 (tpp) cc_final: 0.9226 (mmt) REVERT: AZ 106 GLU cc_start: 0.8786 (pp20) cc_final: 0.8518 (pp20) REVERT: AZ 147 LYS cc_start: 0.9506 (tppp) cc_final: 0.9179 (ttpp) REVERT: BB 13 GLN cc_start: 0.8051 (mt0) cc_final: 0.7741 (mp10) REVERT: BB 24 ASN cc_start: 0.9198 (t0) cc_final: 0.8585 (t0) REVERT: BB 59 ARG cc_start: 0.8447 (mmm160) cc_final: 0.8219 (mmm160) REVERT: BC 3 MET cc_start: 0.8872 (mtp) cc_final: 0.8518 (mtp) REVERT: BC 21 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7933 (mm-30) REVERT: BC 54 GLU cc_start: 0.8573 (pt0) cc_final: 0.7963 (pm20) REVERT: BE 384 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8899 (tp40) REVERT: BH 35 ASP cc_start: 0.9265 (m-30) cc_final: 0.8762 (m-30) REVERT: BH 65 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8187 (tm-30) REVERT: BH 70 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8431 (tm-30) REVERT: BH 74 MET cc_start: 0.8339 (mtm) cc_final: 0.7897 (mtm) REVERT: BH 174 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7342 (pp20) outliers start: 130 outliers final: 58 residues processed: 683 average time/residue: 0.7865 time to fit residues: 639.0295 Evaluate side-chains 630 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 564 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 49 THR Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 67 ARG Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 118 SER Chi-restraints excluded: chain AB residue 128 GLN Chi-restraints excluded: chain AD residue 17 LYS Chi-restraints excluded: chain AD residue 50 THR Chi-restraints excluded: chain AD residue 56 VAL Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 133 ILE Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AF residue 161 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 161 SER Chi-restraints excluded: chain AI residue 36 LEU Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 105 LEU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 151 ASP Chi-restraints excluded: chain AK residue 160 MET Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 54 GLU Chi-restraints excluded: chain AL residue 161 SER Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 139 SER Chi-restraints excluded: chain AS residue 141 VAL Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 66 THR Chi-restraints excluded: chain AV residue 140 LEU Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AZ residue 66 THR Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain BB residue 7 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BC residue 51 VAL Chi-restraints excluded: chain BE residue 212 ASN Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 384 GLN Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Chi-restraints excluded: chain BI residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 234 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 370 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 285 optimal weight: 7.9990 chunk 458 optimal weight: 4.9990 chunk 379 optimal weight: 10.0000 chunk 431 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 117 ASN AD 15 GLN ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AF 10 ASN ** AF 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 128 GLN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047798 restraints weight = 118973.520| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.49 r_work: 0.2822 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37841 Z= 0.142 Angle : 0.618 13.075 51257 Z= 0.300 Chirality : 0.038 0.173 5740 Planarity : 0.004 0.053 6586 Dihedral : 7.895 88.861 6399 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.07 % Favored : 97.91 % Rotamer: Outliers : 3.11 % Allowed : 21.52 % Favored : 75.37 % 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: 1.62 (0.12), residues: 4683 helix: 1.65 (0.09), residues: 3584 sheet: 1.18 (1.09), residues: 26 loop : -0.81 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARGAD 39 TYR 0.023 0.001 TYRBE 597 PHE 0.016 0.001 PHEBE 76 TRP 0.008 0.001 TRPBE 158 HIS 0.002 0.001 HISAE 62 Details of bonding type rmsd covalent geometry : bond 0.00324 (37817) covalent geometry : angle 0.61814 (51257) hydrogen bonds : bond 0.03304 ( 2490) hydrogen bonds : angle 4.03279 ( 7446) Misc. bond : bond 0.00064 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 603 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9436 (p0) cc_final: 0.9153 (p0) REVERT: AA 128 GLN cc_start: 0.8095 (tp40) cc_final: 0.7833 (tp-100) REVERT: AB 28 LYS cc_start: 0.9171 (mmtt) cc_final: 0.8882 (mmmm) REVERT: AB 35 GLU cc_start: 0.8579 (mp0) cc_final: 0.8248 (mp0) REVERT: AB 54 GLU cc_start: 0.9194 (tp30) cc_final: 0.8908 (tp30) REVERT: AB 67 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7155 (mtm110) REVERT: AB 83 ARG cc_start: 0.7347 (ttp80) cc_final: 0.6991 (ttp-170) REVERT: AB 128 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: AC 24 ASP cc_start: 0.8340 (m-30) cc_final: 0.7952 (t0) REVERT: AC 27 LYS cc_start: 0.9213 (ttpt) cc_final: 0.8961 (pptt) REVERT: AC 53 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: AC 60 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8489 (tm-30) REVERT: AC 61 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8545 (ttmt) REVERT: AC 73 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: AC 100 ASP cc_start: 0.7673 (t70) cc_final: 0.7347 (t70) REVERT: AC 133 MET cc_start: 0.7735 (mtt) cc_final: 0.7456 (mtt) REVERT: AC 141 MET cc_start: 0.6731 (ptm) cc_final: 0.6211 (pp-130) REVERT: AD 2 GLN cc_start: 0.8243 (pm20) cc_final: 0.7758 (pm20) REVERT: AD 3 ASP cc_start: 0.7520 (m-30) cc_final: 0.7293 (m-30) REVERT: AD 17 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8579 (ptpp) REVERT: AD 105 ASP cc_start: 0.8850 (m-30) cc_final: 0.8573 (m-30) REVERT: AD 113 LYS cc_start: 0.7741 (tttp) cc_final: 0.7531 (tttm) REVERT: AD 117 ASN cc_start: 0.8783 (m110) cc_final: 0.8548 (m110) REVERT: AD 131 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7722 (tm-30) REVERT: AD 135 GLU cc_start: 0.8614 (mp0) cc_final: 0.8069 (mp0) REVERT: AE 22 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8158 (pt0) REVERT: AE 61 LYS cc_start: 0.9251 (tttp) cc_final: 0.9019 (tttt) REVERT: AE 83 ARG cc_start: 0.8151 (tmm-80) cc_final: 0.7891 (tmm-80) REVERT: AE 113 LYS cc_start: 0.7818 (tppp) cc_final: 0.7576 (mmmm) REVERT: AE 115 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7852 (tmm) REVERT: AF 17 LYS cc_start: 0.7458 (mtmm) cc_final: 0.6962 (mtmm) REVERT: AF 100 ASP cc_start: 0.7893 (t70) cc_final: 0.7271 (t0) REVERT: AF 105 ASP cc_start: 0.8993 (t0) cc_final: 0.8747 (m-30) REVERT: AH 61 LYS cc_start: 0.9666 (mtpp) cc_final: 0.9422 (mtmm) REVERT: AH 100 ASP cc_start: 0.9041 (t0) cc_final: 0.8543 (t0) REVERT: AJ 27 LYS cc_start: 0.9014 (tptt) cc_final: 0.8746 (ttpp) REVERT: AJ 141 MET cc_start: 0.9007 (mtm) cc_final: 0.8332 (ptp) REVERT: AL 54 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8664 (mp0) REVERT: AN 44 THR cc_start: 0.9160 (m) cc_final: 0.8753 (p) REVERT: AQ 149 MET cc_start: 0.9506 (mmm) cc_final: 0.9205 (tpp) REVERT: AS 131 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: AU 24 ASP cc_start: 0.8812 (m-30) cc_final: 0.8554 (m-30) REVERT: AU 27 LYS cc_start: 0.9159 (ptmm) cc_final: 0.8788 (ptpp) REVERT: AU 144 ASP cc_start: 0.8082 (p0) cc_final: 0.7753 (p0) REVERT: AU 145 ASP cc_start: 0.8814 (m-30) cc_final: 0.8587 (m-30) REVERT: AV 1 MET cc_start: 0.8045 (pmm) cc_final: 0.7546 (ppp) REVERT: AV 2 GLN cc_start: 0.8236 (tt0) cc_final: 0.7813 (tm-30) REVERT: AV 15 GLN cc_start: 0.8679 (mp10) cc_final: 0.8341 (mp10) REVERT: AV 35 GLU cc_start: 0.8898 (tp30) cc_final: 0.8386 (tp30) REVERT: AV 39 ARG cc_start: 0.9384 (ptp-110) cc_final: 0.9144 (ptp-110) REVERT: AV 106 GLU cc_start: 0.9089 (tt0) cc_final: 0.8712 (tt0) REVERT: AW 100 ASP cc_start: 0.8465 (t0) cc_final: 0.7696 (t0) REVERT: AX 15 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8563 (pm20) REVERT: AX 54 GLU cc_start: 0.9277 (tt0) cc_final: 0.8856 (tm-30) REVERT: AY 27 LYS cc_start: 0.9027 (tptt) cc_final: 0.8774 (mmmt) REVERT: AY 160 MET cc_start: 0.9467 (tpp) cc_final: 0.9232 (mmt) REVERT: AZ 106 GLU cc_start: 0.8720 (pp20) cc_final: 0.8420 (pp20) REVERT: AZ 147 LYS cc_start: 0.9501 (tppp) cc_final: 0.9193 (ttpp) REVERT: BB 24 ASN cc_start: 0.9197 (t0) cc_final: 0.8592 (t0) REVERT: BC 3 MET cc_start: 0.8922 (mtp) cc_final: 0.8571 (mtp) REVERT: BC 21 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7849 (mm-30) REVERT: BC 54 GLU cc_start: 0.8621 (pt0) cc_final: 0.8041 (pm20) REVERT: BE 384 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8773 (mm-40) REVERT: BG 202 ARG cc_start: 0.9195 (ttm-80) cc_final: 0.8958 (ttm-80) REVERT: BG 249 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7742 (ptp-170) REVERT: BH 65 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8137 (tm-30) REVERT: BH 70 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8413 (tm-30) REVERT: BH 74 MET cc_start: 0.8334 (mtm) cc_final: 0.7859 (mtm) REVERT: BH 174 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7200 (pp20) REVERT: BI 113 MET cc_start: 0.8315 (mtm) cc_final: 0.8051 (mtp) outliers start: 118 outliers final: 46 residues processed: 676 average time/residue: 0.7779 time to fit residues: 626.4241 Evaluate side-chains 618 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 562 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 67 ARG Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 128 GLN Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AD residue 50 THR Chi-restraints excluded: chain AD residue 56 VAL Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AF residue 161 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 102 THR Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 105 LEU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 54 GLU Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AS residue 131 GLN Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 141 VAL Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 66 THR Chi-restraints excluded: chain AV residue 140 LEU Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AX residue 15 GLN Chi-restraints excluded: chain AZ residue 66 THR Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain BB residue 7 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BC residue 51 VAL Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 212 ASN Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 384 GLN Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Chi-restraints excluded: chain BI residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 127 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 240 optimal weight: 7.9990 chunk 313 optimal weight: 0.5980 chunk 330 optimal weight: 0.8980 chunk 292 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 406 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 359 optimal weight: 2.9990 chunk 374 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 117 ASN AD 15 GLN ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AF 128 GLN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.061752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048043 restraints weight = 119235.919| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.42 r_work: 0.2835 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37841 Z= 0.141 Angle : 0.629 12.867 51257 Z= 0.306 Chirality : 0.038 0.202 5740 Planarity : 0.004 0.076 6586 Dihedral : 7.879 87.885 6399 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.05 % Favored : 97.93 % Rotamer: Outliers : 2.53 % Allowed : 22.78 % Favored : 74.68 % 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: 1.71 (0.12), residues: 4683 helix: 1.69 (0.09), residues: 3595 sheet: 1.22 (1.10), residues: 26 loop : -0.73 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARGAD 67 TYR 0.023 0.001 TYRBE 597 PHE 0.017 0.001 PHEBE 76 TRP 0.007 0.001 TRPBE 158 HIS 0.001 0.000 HISAE 62 Details of bonding type rmsd covalent geometry : bond 0.00324 (37817) covalent geometry : angle 0.62925 (51257) hydrogen bonds : bond 0.03253 ( 2490) hydrogen bonds : angle 4.02694 ( 7446) Misc. bond : bond 0.00057 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 584 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9430 (p0) cc_final: 0.9158 (p0) REVERT: AA 128 GLN cc_start: 0.8115 (tp40) cc_final: 0.7883 (tp-100) REVERT: AB 28 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8869 (mmmm) REVERT: AB 35 GLU cc_start: 0.8588 (mp0) cc_final: 0.8239 (mp0) REVERT: AB 54 GLU cc_start: 0.9184 (tp30) cc_final: 0.8883 (tp30) REVERT: AC 24 ASP cc_start: 0.8428 (m-30) cc_final: 0.8045 (t0) REVERT: AC 27 LYS cc_start: 0.9217 (ttpt) cc_final: 0.8963 (pptt) REVERT: AC 56 ASP cc_start: 0.8791 (m-30) cc_final: 0.8507 (m-30) REVERT: AC 60 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8492 (tm-30) REVERT: AC 61 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8572 (ttmt) REVERT: AC 73 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: AC 100 ASP cc_start: 0.7687 (t70) cc_final: 0.7330 (t70) REVERT: AC 133 MET cc_start: 0.7680 (mtt) cc_final: 0.7408 (mtt) REVERT: AC 141 MET cc_start: 0.6659 (ptm) cc_final: 0.6073 (pp-130) REVERT: AD 2 GLN cc_start: 0.8241 (pm20) cc_final: 0.7736 (pm20) REVERT: AD 17 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8529 (ptpp) REVERT: AD 84 ASP cc_start: 0.8743 (m-30) cc_final: 0.8400 (m-30) REVERT: AD 105 ASP cc_start: 0.8835 (m-30) cc_final: 0.8565 (m-30) REVERT: AD 117 ASN cc_start: 0.8804 (m110) cc_final: 0.8590 (m110) REVERT: AD 131 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7632 (tm-30) REVERT: AD 135 GLU cc_start: 0.8622 (mp0) cc_final: 0.8025 (mp0) REVERT: AE 22 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8167 (pt0) REVERT: AE 37 ILE cc_start: 0.8296 (mp) cc_final: 0.8057 (mp) REVERT: AE 41 GLU cc_start: 0.8326 (mp0) cc_final: 0.8120 (mp0) REVERT: AE 60 LYS cc_start: 0.8840 (tmmm) cc_final: 0.8618 (tptp) REVERT: AE 83 ARG cc_start: 0.8147 (tmm-80) cc_final: 0.7876 (tmm-80) REVERT: AE 115 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7865 (tmm) REVERT: AF 15 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7615 (mp-120) REVERT: AF 17 LYS cc_start: 0.7566 (mtmm) cc_final: 0.7288 (mtmm) REVERT: AF 71 ASN cc_start: 0.8329 (t0) cc_final: 0.7792 (t0) REVERT: AF 100 ASP cc_start: 0.7861 (t70) cc_final: 0.7241 (t0) REVERT: AF 105 ASP cc_start: 0.8991 (t0) cc_final: 0.8543 (m-30) REVERT: AH 61 LYS cc_start: 0.9659 (mtpp) cc_final: 0.9412 (mtmm) REVERT: AH 100 ASP cc_start: 0.9023 (t0) cc_final: 0.8525 (t0) REVERT: AI 54 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8955 (mp0) REVERT: AJ 27 LYS cc_start: 0.9015 (tptt) cc_final: 0.8730 (ttpp) REVERT: AJ 141 MET cc_start: 0.9017 (mtm) cc_final: 0.8362 (ptp) REVERT: AK 24 MET cc_start: 0.8663 (mmt) cc_final: 0.8345 (mmt) REVERT: AL 54 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: AN 44 THR cc_start: 0.9137 (m) cc_final: 0.8737 (p) REVERT: AO 28 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8686 (mtmt) REVERT: AQ 149 MET cc_start: 0.9516 (mmm) cc_final: 0.9220 (tpp) REVERT: AS 131 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8355 (mp10) REVERT: AU 24 ASP cc_start: 0.8831 (m-30) cc_final: 0.8584 (m-30) REVERT: AU 27 LYS cc_start: 0.9169 (ptmm) cc_final: 0.8832 (ptpp) REVERT: AU 100 ASP cc_start: 0.8249 (t70) cc_final: 0.7965 (t0) REVERT: AU 144 ASP cc_start: 0.8088 (p0) cc_final: 0.7786 (p0) REVERT: AV 1 MET cc_start: 0.8123 (pmm) cc_final: 0.7631 (ppp) REVERT: AV 15 GLN cc_start: 0.8686 (mp10) cc_final: 0.8355 (mp10) REVERT: AV 35 GLU cc_start: 0.8915 (tp30) cc_final: 0.8439 (tp30) REVERT: AV 39 ARG cc_start: 0.9379 (ptp-110) cc_final: 0.9144 (ptp-110) REVERT: AV 106 GLU cc_start: 0.9080 (tt0) cc_final: 0.8736 (tt0) REVERT: AW 100 ASP cc_start: 0.8488 (t0) cc_final: 0.7723 (t0) REVERT: AX 15 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8606 (pm20) REVERT: AX 54 GLU cc_start: 0.9258 (tt0) cc_final: 0.8848 (tm-30) REVERT: AY 27 LYS cc_start: 0.9015 (tptt) cc_final: 0.8761 (mmmt) REVERT: AY 160 MET cc_start: 0.9468 (tpp) cc_final: 0.9229 (mmt) REVERT: AZ 106 GLU cc_start: 0.8740 (pp20) cc_final: 0.8440 (pp20) REVERT: AZ 147 LYS cc_start: 0.9499 (tppp) cc_final: 0.9186 (ttpp) REVERT: AZ 149 MET cc_start: 0.9446 (mmm) cc_final: 0.8962 (tpt) REVERT: BB 24 ASN cc_start: 0.9184 (t0) cc_final: 0.8587 (t0) REVERT: BC 3 MET cc_start: 0.8950 (mtp) cc_final: 0.8556 (mtp) REVERT: BC 21 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7822 (mm-30) REVERT: BC 54 GLU cc_start: 0.8647 (pt0) cc_final: 0.8068 (pm20) REVERT: BE 384 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8713 (mm110) REVERT: BG 243 GLU cc_start: 0.9354 (tp30) cc_final: 0.9115 (mp0) REVERT: BH 65 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8141 (tm-30) REVERT: BH 70 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8401 (tm-30) REVERT: BH 74 MET cc_start: 0.8333 (mtm) cc_final: 0.7828 (mtm) REVERT: BH 174 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7360 (pp20) REVERT: BI 113 MET cc_start: 0.8337 (mtm) cc_final: 0.8120 (mtp) outliers start: 96 outliers final: 52 residues processed: 642 average time/residue: 0.7660 time to fit residues: 585.9038 Evaluate side-chains 623 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 562 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 118 SER Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AD residue 17 LYS Chi-restraints excluded: chain AD residue 50 THR Chi-restraints excluded: chain AD residue 56 VAL Chi-restraints excluded: chain AD residue 60 LEU Chi-restraints excluded: chain AD residue 66 THR Chi-restraints excluded: chain AD residue 100 ASP Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AF residue 161 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 102 THR Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 105 LEU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 151 ASP Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 54 GLU Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AQ residue 1 MET Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AS residue 131 GLN Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 141 VAL Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 66 THR Chi-restraints excluded: chain AV residue 140 LEU Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AX residue 15 GLN Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 7 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BC residue 51 VAL Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 384 GLN Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 69 LYS Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 160 ASP Chi-restraints excluded: chain BH residue 174 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 357 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 347 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 340 optimal weight: 2.9990 chunk 375 optimal weight: 9.9990 chunk 230 optimal weight: 0.5980 chunk 405 optimal weight: 0.8980 chunk 446 optimal weight: 0.6980 chunk 262 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 117 ASN AD 15 GLN ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AO 10 ASN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 2 GLN BC 13 GLN ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 451 ASN BI 96 GLN BI 97 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.062628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048944 restraints weight = 118534.913| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.47 r_work: 0.2861 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37841 Z= 0.120 Angle : 0.621 13.206 51257 Z= 0.302 Chirality : 0.037 0.179 5740 Planarity : 0.004 0.063 6586 Dihedral : 7.825 87.972 6396 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.80 % Rotamer: Outliers : 2.19 % Allowed : 23.29 % Favored : 74.53 % 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: 1.77 (0.12), residues: 4683 helix: 1.72 (0.09), residues: 3599 sheet: 1.17 (1.10), residues: 26 loop : -0.68 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARGAD 39 TYR 0.021 0.001 TYRBE 597 PHE 0.016 0.001 PHEBE 76 TRP 0.005 0.001 TRPBH 41 HIS 0.001 0.000 HISAE 62 Details of bonding type rmsd covalent geometry : bond 0.00275 (37817) covalent geometry : angle 0.62066 (51257) hydrogen bonds : bond 0.03093 ( 2490) hydrogen bonds : angle 3.99462 ( 7446) Misc. bond : bond 0.00040 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 593 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9410 (p0) cc_final: 0.9153 (p0) REVERT: AB 28 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8894 (mmmm) REVERT: AB 35 GLU cc_start: 0.8591 (mp0) cc_final: 0.8257 (mp0) REVERT: AB 54 GLU cc_start: 0.9187 (tp30) cc_final: 0.8902 (tp30) REVERT: AC 24 ASP cc_start: 0.8434 (m-30) cc_final: 0.7975 (t0) REVERT: AC 27 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8979 (pptt) REVERT: AC 60 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8453 (tm-30) REVERT: AC 61 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8544 (ttmt) REVERT: AC 73 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: AC 100 ASP cc_start: 0.7741 (t70) cc_final: 0.7352 (t70) REVERT: AC 141 MET cc_start: 0.6558 (ptm) cc_final: 0.6031 (pp-130) REVERT: AD 2 GLN cc_start: 0.8193 (pm20) cc_final: 0.7748 (pm20) REVERT: AD 17 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8547 (ptpp) REVERT: AD 105 ASP cc_start: 0.8789 (m-30) cc_final: 0.8537 (m-30) REVERT: AD 117 ASN cc_start: 0.8834 (m110) cc_final: 0.8591 (m110) REVERT: AE 22 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8153 (pt0) REVERT: AE 37 ILE cc_start: 0.8494 (mp) cc_final: 0.8194 (mp) REVERT: AE 41 GLU cc_start: 0.8320 (mp0) cc_final: 0.8114 (mp0) REVERT: AE 60 LYS cc_start: 0.8852 (tmmm) cc_final: 0.8600 (tptp) REVERT: AE 83 ARG cc_start: 0.8097 (tmm-80) cc_final: 0.7873 (tmm-80) REVERT: AE 115 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7894 (tmm) REVERT: AF 15 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7557 (mp-120) REVERT: AF 17 LYS cc_start: 0.7557 (mtmm) cc_final: 0.7303 (mtmm) REVERT: AF 71 ASN cc_start: 0.8309 (t0) cc_final: 0.7846 (t0) REVERT: AF 100 ASP cc_start: 0.7798 (t70) cc_final: 0.7203 (t0) REVERT: AF 105 ASP cc_start: 0.8902 (t0) cc_final: 0.8311 (m-30) REVERT: AH 61 LYS cc_start: 0.9653 (mtpp) cc_final: 0.9437 (mtmm) REVERT: AH 100 ASP cc_start: 0.9039 (t0) cc_final: 0.8576 (t0) REVERT: AH 115 MET cc_start: 0.9682 (ttt) cc_final: 0.9468 (ttp) REVERT: AH 161 SER cc_start: 0.8319 (m) cc_final: 0.7824 (p) REVERT: AI 54 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8971 (mp0) REVERT: AJ 141 MET cc_start: 0.9013 (mtm) cc_final: 0.8365 (ptp) REVERT: AK 24 MET cc_start: 0.8707 (mmt) cc_final: 0.8352 (mmt) REVERT: AL 54 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: AN 44 THR cc_start: 0.9036 (m) cc_final: 0.8671 (p) REVERT: AO 24 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.7978 (mpt) REVERT: AO 28 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8853 (mtmm) REVERT: AR 24 ASP cc_start: 0.9268 (t0) cc_final: 0.9060 (t0) REVERT: AS 131 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8359 (mp10) REVERT: AU 27 LYS cc_start: 0.9147 (ptmm) cc_final: 0.8789 (ptpp) REVERT: AU 145 ASP cc_start: 0.8729 (m-30) cc_final: 0.8453 (m-30) REVERT: AV 1 MET cc_start: 0.8043 (pmm) cc_final: 0.7623 (ppp) REVERT: AV 2 GLN cc_start: 0.8396 (tt0) cc_final: 0.8156 (tm-30) REVERT: AV 15 GLN cc_start: 0.8678 (mp10) cc_final: 0.8220 (mp10) REVERT: AV 35 GLU cc_start: 0.8844 (tp30) cc_final: 0.8358 (tp30) REVERT: AV 39 ARG cc_start: 0.9413 (ptp-110) cc_final: 0.9148 (ptp-110) REVERT: AV 106 GLU cc_start: 0.9088 (tt0) cc_final: 0.8749 (tt0) REVERT: AW 100 ASP cc_start: 0.8492 (t0) cc_final: 0.7687 (t0) REVERT: AX 15 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: AX 54 GLU cc_start: 0.9275 (tt0) cc_final: 0.8861 (tm-30) REVERT: AY 27 LYS cc_start: 0.9003 (tptt) cc_final: 0.8753 (mmmt) REVERT: AY 160 MET cc_start: 0.9464 (tpp) cc_final: 0.9213 (mmt) REVERT: AZ 35 GLU cc_start: 0.8532 (mp0) cc_final: 0.8311 (mp0) REVERT: AZ 106 GLU cc_start: 0.8743 (pp20) cc_final: 0.8411 (pp20) REVERT: AZ 147 LYS cc_start: 0.9494 (tppp) cc_final: 0.9193 (ttpp) REVERT: AZ 149 MET cc_start: 0.9439 (mmm) cc_final: 0.8884 (tpt) REVERT: BB 24 ASN cc_start: 0.9180 (t0) cc_final: 0.8602 (t0) REVERT: BC 3 MET cc_start: 0.8928 (mtp) cc_final: 0.8520 (mtp) REVERT: BC 21 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7810 (mm-30) REVERT: BC 54 GLU cc_start: 0.8670 (pt0) cc_final: 0.8090 (pm20) REVERT: BE 202 MET cc_start: 0.9082 (mtt) cc_final: 0.8724 (mtt) REVERT: BG 243 GLU cc_start: 0.9352 (tp30) cc_final: 0.9101 (mp0) REVERT: BG 249 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7807 (ptp-170) REVERT: BH 65 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8099 (tm-30) REVERT: BH 70 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8396 (tm-30) REVERT: BH 74 MET cc_start: 0.8320 (mtm) cc_final: 0.7821 (mtm) REVERT: BI 113 MET cc_start: 0.8280 (mtm) cc_final: 0.7993 (mtp) outliers start: 83 outliers final: 44 residues processed: 646 average time/residue: 0.7850 time to fit residues: 602.4086 Evaluate side-chains 615 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 563 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 118 SER Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AC residue 77 MET Chi-restraints excluded: chain AD residue 17 LYS Chi-restraints excluded: chain AD residue 50 THR Chi-restraints excluded: chain AD residue 60 LEU Chi-restraints excluded: chain AD residue 100 ASP Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 102 THR Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 151 ASP Chi-restraints excluded: chain AL residue 54 GLU Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AO residue 24 MET Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AQ residue 1 MET Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AS residue 131 GLN Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 140 LEU Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AX residue 15 GLN Chi-restraints excluded: chain AZ residue 66 THR Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 7 THR Chi-restraints excluded: chain BB residue 16 ILE Chi-restraints excluded: chain BB residue 46 MET Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BC residue 51 VAL Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 69 LYS Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 160 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 428 optimal weight: 0.0970 chunk 58 optimal weight: 8.9990 chunk 301 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 311 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 260 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 117 ASN AD 15 GLN AD 131 GLN ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 128 GLN BB 19 GLN BC 41 GLN ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.062951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049234 restraints weight = 119020.069| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.55 r_work: 0.2870 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37841 Z= 0.125 Angle : 0.635 12.895 51257 Z= 0.311 Chirality : 0.038 0.462 5740 Planarity : 0.004 0.098 6586 Dihedral : 7.826 89.589 6393 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 2.03 % Allowed : 23.68 % Favored : 74.29 % 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: 1.80 (0.12), residues: 4683 helix: 1.74 (0.09), residues: 3598 sheet: 1.20 (1.12), residues: 26 loop : -0.66 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARGAD 67 TYR 0.021 0.001 TYRBE 597 PHE 0.028 0.001 PHEBE 76 TRP 0.007 0.001 TRPBB 36 HIS 0.003 0.001 HISAE 62 Details of bonding type rmsd covalent geometry : bond 0.00287 (37817) covalent geometry : angle 0.63497 (51257) hydrogen bonds : bond 0.03056 ( 2490) hydrogen bonds : angle 3.98987 ( 7446) Misc. bond : bond 0.00041 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 583 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9400 (p0) cc_final: 0.9148 (p0) REVERT: AB 15 GLN cc_start: 0.8786 (mp10) cc_final: 0.8288 (mp10) REVERT: AB 28 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8857 (mmmm) REVERT: AB 35 GLU cc_start: 0.8573 (mp0) cc_final: 0.8241 (mp0) REVERT: AB 54 GLU cc_start: 0.9139 (tp30) cc_final: 0.8838 (tp30) REVERT: AC 24 ASP cc_start: 0.8411 (m-30) cc_final: 0.7893 (t0) REVERT: AC 27 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8972 (pptt) REVERT: AC 73 TYR cc_start: 0.6451 (OUTLIER) cc_final: 0.6202 (m-80) REVERT: AC 85 MET cc_start: 0.7903 (mmm) cc_final: 0.7453 (mtp) REVERT: AC 100 ASP cc_start: 0.7697 (t70) cc_final: 0.7363 (t70) REVERT: AC 141 MET cc_start: 0.6407 (ptm) cc_final: 0.5576 (pp-130) REVERT: AD 2 GLN cc_start: 0.8125 (pm20) cc_final: 0.7716 (pm20) REVERT: AD 17 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8466 (ptpp) REVERT: AD 58 LYS cc_start: 0.8880 (ptpt) cc_final: 0.8676 (ptpp) REVERT: AD 84 ASP cc_start: 0.8776 (m-30) cc_final: 0.8543 (m-30) REVERT: AD 105 ASP cc_start: 0.8764 (m-30) cc_final: 0.8513 (m-30) REVERT: AD 117 ASN cc_start: 0.8814 (m110) cc_final: 0.8558 (m110) REVERT: AD 135 GLU cc_start: 0.8614 (mp0) cc_final: 0.8313 (mp0) REVERT: AE 22 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8138 (pt0) REVERT: AE 37 ILE cc_start: 0.8503 (mp) cc_final: 0.8219 (mp) REVERT: AE 83 ARG cc_start: 0.8007 (tmm-80) cc_final: 0.7780 (tmm-80) REVERT: AE 115 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7854 (tpt) REVERT: AF 15 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: AF 17 LYS cc_start: 0.7540 (mtmm) cc_final: 0.7333 (mtmm) REVERT: AF 20 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8599 (p0) REVERT: AF 71 ASN cc_start: 0.8102 (t0) cc_final: 0.7661 (t0) REVERT: AF 100 ASP cc_start: 0.7640 (t70) cc_final: 0.7053 (t0) REVERT: AF 105 ASP cc_start: 0.8785 (t0) cc_final: 0.8160 (m-30) REVERT: AH 61 LYS cc_start: 0.9624 (mtpp) cc_final: 0.9410 (mtmm) REVERT: AH 100 ASP cc_start: 0.8863 (t0) cc_final: 0.8391 (t0) REVERT: AH 161 SER cc_start: 0.8213 (m) cc_final: 0.7742 (p) REVERT: AI 54 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8754 (mp0) REVERT: AJ 141 MET cc_start: 0.8923 (mtm) cc_final: 0.8174 (ptp) REVERT: AK 24 MET cc_start: 0.8573 (mmt) cc_final: 0.8198 (mmt) REVERT: AN 44 THR cc_start: 0.8964 (m) cc_final: 0.8602 (p) REVERT: AO 24 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8634 (mpp) REVERT: AO 28 LYS cc_start: 0.9028 (mtmm) cc_final: 0.8742 (mtmm) REVERT: AS 131 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8245 (mp10) REVERT: AU 24 ASP cc_start: 0.8693 (m-30) cc_final: 0.8421 (m-30) REVERT: AU 27 LYS cc_start: 0.9106 (ptmm) cc_final: 0.8756 (ptpp) REVERT: AU 53 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: AV 2 GLN cc_start: 0.8432 (tt0) cc_final: 0.8213 (tm-30) REVERT: AV 15 GLN cc_start: 0.8610 (mp10) cc_final: 0.8145 (mp10) REVERT: AV 35 GLU cc_start: 0.8738 (tp30) cc_final: 0.8291 (tp30) REVERT: AV 39 ARG cc_start: 0.9360 (ptp-110) cc_final: 0.9068 (ptp-110) REVERT: AV 45 SER cc_start: 0.8429 (m) cc_final: 0.8195 (t) REVERT: AV 106 GLU cc_start: 0.9000 (tt0) cc_final: 0.8630 (tt0) REVERT: AW 100 ASP cc_start: 0.8346 (t0) cc_final: 0.7620 (t0) REVERT: AX 15 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8551 (pm20) REVERT: AX 54 GLU cc_start: 0.9150 (tt0) cc_final: 0.8759 (tm-30) REVERT: AZ 106 GLU cc_start: 0.8552 (pp20) cc_final: 0.8205 (pp20) REVERT: AZ 147 LYS cc_start: 0.9470 (tppp) cc_final: 0.9189 (ttpp) REVERT: AZ 149 MET cc_start: 0.9349 (mmm) cc_final: 0.8739 (tpt) REVERT: BB 24 ASN cc_start: 0.9100 (t0) cc_final: 0.8517 (t0) REVERT: BB 54 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7446 (mm-30) REVERT: BC 3 MET cc_start: 0.8912 (mtp) cc_final: 0.8497 (mtp) REVERT: BC 21 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7650 (mm-30) REVERT: BC 44 MET cc_start: 0.7449 (mtt) cc_final: 0.6897 (mtt) REVERT: BC 54 GLU cc_start: 0.8606 (pt0) cc_final: 0.8068 (pm20) REVERT: BE 202 MET cc_start: 0.8928 (mtt) cc_final: 0.8541 (mtt) REVERT: BE 384 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8542 (mm-40) REVERT: BG 243 GLU cc_start: 0.9266 (tp30) cc_final: 0.9054 (mp0) REVERT: BG 249 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7774 (ptp-170) REVERT: BH 65 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7970 (tm-30) REVERT: BH 70 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8189 (tm-30) REVERT: BH 74 MET cc_start: 0.8204 (mtm) cc_final: 0.7714 (mtp) REVERT: BH 174 GLU cc_start: 0.7463 (pt0) cc_final: 0.6891 (pp20) outliers start: 77 outliers final: 42 residues processed: 629 average time/residue: 0.8169 time to fit residues: 609.9778 Evaluate side-chains 615 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 563 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 118 SER Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AC residue 77 MET Chi-restraints excluded: chain AD residue 17 LYS Chi-restraints excluded: chain AD residue 50 THR Chi-restraints excluded: chain AD residue 60 LEU Chi-restraints excluded: chain AD residue 100 ASP Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 102 THR Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 151 ASP Chi-restraints excluded: chain AL residue 54 GLU Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AO residue 24 MET Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AQ residue 1 MET Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AS residue 131 GLN Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AU residue 53 GLN Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 140 LEU Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AX residue 15 GLN Chi-restraints excluded: chain AZ residue 66 THR Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 7 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 384 GLN Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 69 LYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 160 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 21 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 316 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 117 ASN AD 15 GLN ** AD 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AN 128 GLN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 128 GLN BB 63 ASN BC 13 GLN ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048149 restraints weight = 118257.713| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.57 r_work: 0.2830 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 37841 Z= 0.166 Angle : 0.670 12.381 51257 Z= 0.329 Chirality : 0.039 0.451 5740 Planarity : 0.004 0.080 6586 Dihedral : 7.728 87.965 6393 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 1.77 % Allowed : 24.34 % Favored : 73.89 % 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: 1.82 (0.12), residues: 4683 helix: 1.76 (0.09), residues: 3591 sheet: 1.24 (1.14), residues: 26 loop : -0.63 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARGAD 39 TYR 0.023 0.001 TYRBE 597 PHE 0.016 0.001 PHEAC 155 TRP 0.009 0.001 TRPBE 158 HIS 0.002 0.001 HISBE 349 Details of bonding type rmsd covalent geometry : bond 0.00385 (37817) covalent geometry : angle 0.66959 (51257) hydrogen bonds : bond 0.03248 ( 2490) hydrogen bonds : angle 4.01915 ( 7446) Misc. bond : bond 0.00075 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 565 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9401 (p0) cc_final: 0.9150 (p0) REVERT: AA 128 GLN cc_start: 0.8178 (tp40) cc_final: 0.7943 (tp-100) REVERT: AB 15 GLN cc_start: 0.8868 (mp10) cc_final: 0.8513 (mp10) REVERT: AB 35 GLU cc_start: 0.8604 (mp0) cc_final: 0.8284 (mp0) REVERT: AB 54 GLU cc_start: 0.9151 (tp30) cc_final: 0.8861 (tp30) REVERT: AC 24 ASP cc_start: 0.8420 (m-30) cc_final: 0.7996 (t0) REVERT: AC 27 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8979 (pptt) REVERT: AC 53 GLN cc_start: 0.7939 (mp10) cc_final: 0.7699 (mp10) REVERT: AC 60 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8440 (tm-30) REVERT: AC 73 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: AC 100 ASP cc_start: 0.7861 (t70) cc_final: 0.7367 (t70) REVERT: AC 141 MET cc_start: 0.6443 (ptm) cc_final: 0.5696 (pp-130) REVERT: AD 17 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8474 (ptpp) REVERT: AD 58 LYS cc_start: 0.8902 (ptpt) cc_final: 0.8672 (ptpp) REVERT: AD 105 ASP cc_start: 0.8812 (m-30) cc_final: 0.8533 (m-30) REVERT: AD 117 ASN cc_start: 0.8828 (m110) cc_final: 0.8577 (m110) REVERT: AE 22 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8152 (pt0) REVERT: AE 83 ARG cc_start: 0.8026 (tmm-80) cc_final: 0.7784 (tmm-80) REVERT: AF 15 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: AF 17 LYS cc_start: 0.7513 (mtmm) cc_final: 0.7308 (mtmm) REVERT: AF 20 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8648 (p0) REVERT: AF 71 ASN cc_start: 0.8309 (t0) cc_final: 0.7856 (t0) REVERT: AF 100 ASP cc_start: 0.7647 (t70) cc_final: 0.7072 (t0) REVERT: AF 105 ASP cc_start: 0.8823 (t0) cc_final: 0.8209 (m-30) REVERT: AH 61 LYS cc_start: 0.9602 (mtpp) cc_final: 0.9362 (mtmm) REVERT: AH 100 ASP cc_start: 0.8869 (t0) cc_final: 0.8418 (t0) REVERT: AI 54 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8792 (mp0) REVERT: AJ 141 MET cc_start: 0.8965 (mtm) cc_final: 0.8192 (ptp) REVERT: AL 54 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8522 (mp0) REVERT: AN 44 THR cc_start: 0.9025 (m) cc_final: 0.8663 (p) REVERT: AO 28 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8756 (mtmm) REVERT: AS 96 MET cc_start: 0.9236 (ttp) cc_final: 0.9035 (ptm) REVERT: AS 131 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: AU 24 ASP cc_start: 0.8722 (m-30) cc_final: 0.8459 (m-30) REVERT: AU 27 LYS cc_start: 0.9107 (ptmm) cc_final: 0.8737 (ptpp) REVERT: AU 100 ASP cc_start: 0.8228 (t70) cc_final: 0.7926 (t0) REVERT: AV 1 MET cc_start: 0.7881 (pmm) cc_final: 0.7483 (ppp) REVERT: AV 2 GLN cc_start: 0.8419 (tt0) cc_final: 0.8136 (tm-30) REVERT: AV 15 GLN cc_start: 0.8596 (mp10) cc_final: 0.8269 (mp10) REVERT: AV 35 GLU cc_start: 0.8797 (tp30) cc_final: 0.8334 (tp30) REVERT: AV 39 ARG cc_start: 0.9338 (ptp-110) cc_final: 0.9040 (ptp-110) REVERT: AV 45 SER cc_start: 0.8547 (m) cc_final: 0.8320 (t) REVERT: AV 106 GLU cc_start: 0.8973 (tt0) cc_final: 0.8585 (tt0) REVERT: AW 100 ASP cc_start: 0.8223 (t0) cc_final: 0.7703 (t0) REVERT: AW 128 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: AX 15 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8585 (pm20) REVERT: AX 54 GLU cc_start: 0.9155 (tt0) cc_final: 0.8770 (tm-30) REVERT: AY 27 LYS cc_start: 0.8961 (tptt) cc_final: 0.8746 (mmmt) REVERT: AY 160 MET cc_start: 0.9455 (tpp) cc_final: 0.9161 (mmt) REVERT: AZ 106 GLU cc_start: 0.8568 (pp20) cc_final: 0.8220 (pp20) REVERT: AZ 114 GLU cc_start: 0.8986 (mp0) cc_final: 0.8712 (mp0) REVERT: AZ 147 LYS cc_start: 0.9456 (tppp) cc_final: 0.9170 (ttpp) REVERT: AZ 149 MET cc_start: 0.9326 (mmm) cc_final: 0.8698 (tpt) REVERT: BB 24 ASN cc_start: 0.9113 (t0) cc_final: 0.8544 (t0) REVERT: BB 54 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7609 (mm-30) REVERT: BC 3 MET cc_start: 0.8878 (mtp) cc_final: 0.8444 (mtp) REVERT: BC 21 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7728 (mm-30) REVERT: BC 44 MET cc_start: 0.7538 (mtt) cc_final: 0.6980 (mtt) REVERT: BC 54 GLU cc_start: 0.8617 (pt0) cc_final: 0.8053 (pm20) REVERT: BE 202 MET cc_start: 0.8974 (mtt) cc_final: 0.8619 (mtt) REVERT: BH 65 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7990 (tm-30) REVERT: BH 70 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8191 (tm-30) REVERT: BH 74 MET cc_start: 0.8194 (mtm) cc_final: 0.7695 (mtp) REVERT: BH 174 GLU cc_start: 0.7550 (pt0) cc_final: 0.6916 (pp20) outliers start: 67 outliers final: 40 residues processed: 608 average time/residue: 0.8035 time to fit residues: 581.4772 Evaluate side-chains 605 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 558 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 118 SER Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AC residue 77 MET Chi-restraints excluded: chain AD residue 60 LEU Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 102 THR Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 105 LEU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 151 ASP Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 54 GLU Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AQ residue 1 MET Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AS residue 131 GLN Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 141 VAL Chi-restraints excluded: chain AU residue 53 GLN Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 140 LEU Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AW residue 128 GLN Chi-restraints excluded: chain AX residue 15 GLN Chi-restraints excluded: chain AZ residue 66 THR Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 7 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 160 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 53 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 438 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 328 optimal weight: 4.9990 chunk 432 optimal weight: 0.9990 chunk 424 optimal weight: 0.3980 chunk 191 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 53 GLN AB 117 ASN AD 15 GLN ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN ** AO 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.062855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049099 restraints weight = 117731.127| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.54 r_work: 0.2859 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37841 Z= 0.130 Angle : 0.652 12.435 51257 Z= 0.322 Chirality : 0.039 0.446 5740 Planarity : 0.004 0.081 6586 Dihedral : 7.796 87.868 6393 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Rotamer: Outliers : 1.66 % Allowed : 24.37 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.80 (0.12), residues: 4683 helix: 1.72 (0.09), residues: 3608 sheet: 1.18 (1.14), residues: 26 loop : -0.59 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARGAD 39 TYR 0.022 0.001 TYRBE 597 PHE 0.014 0.001 PHEAC 155 TRP 0.006 0.001 TRPBH 41 HIS 0.001 0.000 HISAE 62 Details of bonding type rmsd covalent geometry : bond 0.00303 (37817) covalent geometry : angle 0.65184 (51257) hydrogen bonds : bond 0.03114 ( 2490) hydrogen bonds : angle 4.02777 ( 7446) Misc. bond : bond 0.00044 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17555.39 seconds wall clock time: 298 minutes 38.65 seconds (17918.65 seconds total)