Starting phenix.real_space_refine on Tue Aug 26 03:20:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nqd_49649/08_2025/9nqd_49649.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nqd_49649/08_2025/9nqd_49649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nqd_49649/08_2025/9nqd_49649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nqd_49649/08_2025/9nqd_49649.map" model { file = "/net/cci-nas-00/data/ceres_data/9nqd_49649/08_2025/9nqd_49649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nqd_49649/08_2025/9nqd_49649.cif" } resolution = 3.3 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= 0.002 sd= 0.010 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: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 10224 2.51 5 N 3204 2.21 5 O 3792 1.98 5 H 16380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33612 Number of models: 1 Model: "" Number of chains: 1 Chain: "3" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 2801 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 2, 'TRANS': 202} Restraints were copied for chains: 4, 5, 6, 7, 8, 9, 0, AA, AB, AC, AD Time building chain proxies: 3.86, per 1000 atoms: 0.11 Number of scatterers: 33612 At special positions: 0 Unit cell: (86.4, 101.52, 193.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 3792 8.00 N 3204 7.00 C 10224 6.00 H 16380 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 4 sheets defined 2.9% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain '3' and resid 36 through 41 removed outlier: 4.356A pdb=" N THR 3 39 " --> pdb=" O PRO 3 36 " (cutoff:3.500A) Processing helix chain '4' and resid 36 through 41 removed outlier: 4.356A pdb=" N THR 4 39 " --> pdb=" O PRO 4 36 " (cutoff:3.500A) Processing helix chain '5' and resid 36 through 41 removed outlier: 4.356A pdb=" N THR 5 39 " --> pdb=" O PRO 5 36 " (cutoff:3.500A) Processing helix chain '6' and resid 36 through 41 removed outlier: 4.356A pdb=" N THR 6 39 " --> pdb=" O PRO 6 36 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 41 removed outlier: 4.357A pdb=" N THR 7 39 " --> pdb=" O PRO 7 36 " (cutoff:3.500A) Processing helix chain '8' and resid 36 through 41 removed outlier: 4.356A pdb=" N THR 8 39 " --> pdb=" O PRO 8 36 " (cutoff:3.500A) Processing helix chain '9' and resid 36 through 41 removed outlier: 4.357A pdb=" N THR 9 39 " --> pdb=" O PRO 9 36 " (cutoff:3.500A) Processing helix chain '0' and resid 36 through 41 removed outlier: 4.357A pdb=" N THR 0 39 " --> pdb=" O PRO 0 36 " (cutoff:3.500A) Processing helix chain 'AA' and resid 36 through 41 removed outlier: 4.357A pdb=" N THRAA 39 " --> pdb=" O PROAA 36 " (cutoff:3.500A) Processing helix chain 'AB' and resid 36 through 41 removed outlier: 4.356A pdb=" N THRAB 39 " --> pdb=" O PROAB 36 " (cutoff:3.500A) Processing helix chain 'AC' and resid 36 through 41 removed outlier: 4.356A pdb=" N THRAC 39 " --> pdb=" O PROAC 36 " (cutoff:3.500A) Processing helix chain 'AD' and resid 36 through 41 removed outlier: 4.356A pdb=" N THRAD 39 " --> pdb=" O PROAD 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '3' and resid 47 through 57 removed outlier: 6.106A pdb=" N THR 3 47 " --> pdb=" O GLN 3 113 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER 3 115 " --> pdb=" O THR 3 47 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL 3 49 " --> pdb=" O SER 3 115 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ASP 3 117 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS 3 51 " --> pdb=" O ASP 3 117 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 111 through 117 current: chain '4' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 111 through 117 current: chain '5' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 111 through 117 current: chain '6' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 111 through 117 current: chain '7' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 111 through 117 current: chain '8' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain '8' and resid 111 through 117 current: chain '9' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain '9' and resid 111 through 117 current: chain '0' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 111 through 117 current: chain 'AA' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain 'AA' and resid 111 through 117 current: chain 'AB' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain 'AB' and resid 111 through 117 current: chain 'AC' and resid 111 through 117 WARNING: can't find start of bonding for strands! previous: chain 'AC' and resid 111 through 117 current: chain 'AD' and resid 112 through 116 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '3' and resid 198 through 201 removed outlier: 5.671A pdb=" N ASN 3 128 " --> pdb=" O ALA 4 202 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU 4 204 " --> pdb=" O ASN 3 128 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU 3 130 " --> pdb=" O LEU 4 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY 4 203 " --> pdb=" O ALA 4 64 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN 4 128 " --> pdb=" O ALA 5 202 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU 5 204 " --> pdb=" O ASN 4 128 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU 4 130 " --> pdb=" O LEU 5 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY 5 203 " --> pdb=" O ALA 5 64 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN 5 128 " --> pdb=" O ALA 6 202 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU 6 204 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU 5 130 " --> pdb=" O LEU 6 204 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY 6 203 " --> pdb=" O ALA 6 64 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN 6 128 " --> pdb=" O ALA 7 202 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU 7 204 " --> pdb=" O ASN 6 128 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU 6 130 " --> pdb=" O LEU 7 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY 7 203 " --> pdb=" O ALA 7 64 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN 7 128 " --> pdb=" O ALA 8 202 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU 8 204 " --> pdb=" O ASN 7 128 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU 7 130 " --> pdb=" O LEU 8 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY 8 203 " --> pdb=" O ALA 8 64 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN 8 128 " --> pdb=" O ALA 9 202 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU 9 204 " --> pdb=" O ASN 8 128 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU 8 130 " --> pdb=" O LEU 9 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY 9 203 " --> pdb=" O ALA 9 64 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASN 9 128 " --> pdb=" O ALA 0 202 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU 0 204 " --> pdb=" O ASN 9 128 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU 9 130 " --> pdb=" O LEU 0 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY 0 203 " --> pdb=" O ALA 0 64 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASN 0 128 " --> pdb=" O ALAAA 202 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEUAA 204 " --> pdb=" O ASN 0 128 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU 0 130 " --> pdb=" O LEUAA 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLYAA 203 " --> pdb=" O ALAAA 64 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASNAA 128 " --> pdb=" O ALAAB 202 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEUAB 204 " --> pdb=" O ASNAA 128 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEUAA 130 " --> pdb=" O LEUAB 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLYAB 203 " --> pdb=" O ALAAB 64 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASNAB 128 " --> pdb=" O ALAAC 202 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEUAC 204 " --> pdb=" O ASNAB 128 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEUAB 130 " --> pdb=" O LEUAC 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLYAC 203 " --> pdb=" O ALAAC 64 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASNAC 128 " --> pdb=" O ALAAD 202 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEUAD 204 " --> pdb=" O ASNAC 128 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEUAC 130 " --> pdb=" O LEUAD 204 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLYAD 203 " --> pdb=" O ALAAD 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 212 through 221 removed outlier: 6.146A pdb=" N GLY 3 75 " --> pdb=" O ASN 3 214 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY 3 216 " --> pdb=" O GLY 3 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU 3 77 " --> pdb=" O GLY 3 216 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN 3 218 " --> pdb=" O LEU 3 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALA 3 79 " --> pdb=" O ASN 3 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA 3 220 " --> pdb=" O ALA 3 79 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE 3 81 " --> pdb=" O ALA 3 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY 4 213 " --> pdb=" O SER 3 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL 4 219 " --> pdb=" O ASN 3 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA 4 221 " --> pdb=" O ALA 3 147 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY 4 75 " --> pdb=" O ASN 4 214 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY 4 216 " --> pdb=" O GLY 4 75 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU 4 77 " --> pdb=" O GLY 4 216 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN 4 218 " --> pdb=" O LEU 4 77 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA 4 79 " --> pdb=" O ASN 4 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA 4 220 " --> pdb=" O ALA 4 79 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE 4 81 " --> pdb=" O ALA 4 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY 5 213 " --> pdb=" O SER 4 139 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL 5 219 " --> pdb=" O ASN 4 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA 5 221 " --> pdb=" O ALA 4 147 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY 5 75 " --> pdb=" O ASN 5 214 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY 5 216 " --> pdb=" O GLY 5 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU 5 77 " --> pdb=" O GLY 5 216 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN 5 218 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALA 5 79 " --> pdb=" O ASN 5 218 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA 5 220 " --> pdb=" O ALA 5 79 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE 5 81 " --> pdb=" O ALA 5 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY 6 213 " --> pdb=" O SER 5 139 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL 6 219 " --> pdb=" O ASN 5 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA 6 221 " --> pdb=" O ALA 5 147 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY 6 75 " --> pdb=" O ASN 6 214 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY 6 216 " --> pdb=" O GLY 6 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU 6 77 " --> pdb=" O GLY 6 216 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN 6 218 " --> pdb=" O LEU 6 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALA 6 79 " --> pdb=" O ASN 6 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA 6 220 " --> pdb=" O ALA 6 79 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE 6 81 " --> pdb=" O ALA 6 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY 7 213 " --> pdb=" O SER 6 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL 7 219 " --> pdb=" O ASN 6 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA 7 221 " --> pdb=" O ALA 6 147 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY 7 75 " --> pdb=" O ASN 7 214 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY 7 216 " --> pdb=" O GLY 7 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU 7 77 " --> pdb=" O GLY 7 216 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN 7 218 " --> pdb=" O LEU 7 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALA 7 79 " --> pdb=" O ASN 7 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA 7 220 " --> pdb=" O ALA 7 79 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE 7 81 " --> pdb=" O ALA 7 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY 8 213 " --> pdb=" O SER 7 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL 8 219 " --> pdb=" O ASN 7 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA 8 221 " --> pdb=" O ALA 7 147 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY 8 75 " --> pdb=" O ASN 8 214 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY 8 216 " --> pdb=" O GLY 8 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU 8 77 " --> pdb=" O GLY 8 216 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN 8 218 " --> pdb=" O LEU 8 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALA 8 79 " --> pdb=" O ASN 8 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA 8 220 " --> pdb=" O ALA 8 79 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE 8 81 " --> pdb=" O ALA 8 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY 9 213 " --> pdb=" O SER 8 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL 9 219 " --> pdb=" O ASN 8 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA 9 221 " --> pdb=" O ALA 8 147 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY 9 75 " --> pdb=" O ASN 9 214 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY 9 216 " --> pdb=" O GLY 9 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU 9 77 " --> pdb=" O GLY 9 216 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN 9 218 " --> pdb=" O LEU 9 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALA 9 79 " --> pdb=" O ASN 9 218 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA 9 220 " --> pdb=" O ALA 9 79 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE 9 81 " --> pdb=" O ALA 9 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY 0 213 " --> pdb=" O SER 9 139 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL 0 219 " --> pdb=" O ASN 9 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA 0 221 " --> pdb=" O ALA 9 147 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY 0 75 " --> pdb=" O ASN 0 214 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY 0 216 " --> pdb=" O GLY 0 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU 0 77 " --> pdb=" O GLY 0 216 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN 0 218 " --> pdb=" O LEU 0 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALA 0 79 " --> pdb=" O ASN 0 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA 0 220 " --> pdb=" O ALA 0 79 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE 0 81 " --> pdb=" O ALA 0 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLYAA 213 " --> pdb=" O SER 0 139 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VALAA 219 " --> pdb=" O ASN 0 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALAAA 221 " --> pdb=" O ALA 0 147 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLYAA 75 " --> pdb=" O ASNAA 214 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLYAA 216 " --> pdb=" O GLYAA 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEUAA 77 " --> pdb=" O GLYAA 216 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASNAA 218 " --> pdb=" O LEUAA 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALAAA 79 " --> pdb=" O ASNAA 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALAAA 220 " --> pdb=" O ALAAA 79 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILEAA 81 " --> pdb=" O ALAAA 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLYAB 213 " --> pdb=" O SERAA 139 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VALAB 219 " --> pdb=" O ASNAA 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALAAB 221 " --> pdb=" O ALAAA 147 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLYAB 75 " --> pdb=" O ASNAB 214 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLYAB 216 " --> pdb=" O GLYAB 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEUAB 77 " --> pdb=" O GLYAB 216 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASNAB 218 " --> pdb=" O LEUAB 77 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALAAB 79 " --> pdb=" O ASNAB 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALAAB 220 " --> pdb=" O ALAAB 79 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILEAB 81 " --> pdb=" O ALAAB 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLYAC 213 " --> pdb=" O SERAB 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VALAC 219 " --> pdb=" O ASNAB 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALAAC 221 " --> pdb=" O ALAAB 147 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLYAC 75 " --> pdb=" O ASNAC 214 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLYAC 216 " --> pdb=" O GLYAC 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEUAC 77 " --> pdb=" O GLYAC 216 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASNAC 218 " --> pdb=" O LEUAC 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALAAC 79 " --> pdb=" O ASNAC 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALAAC 220 " --> pdb=" O ALAAC 79 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILEAC 81 " --> pdb=" O ALAAC 220 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLYAD 213 " --> pdb=" O SERAC 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VALAD 219 " --> pdb=" O ASNAC 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALAAD 221 " --> pdb=" O ALAAC 147 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLYAD 75 " --> pdb=" O ASNAD 214 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLYAD 216 " --> pdb=" O GLYAD 75 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEUAD 77 " --> pdb=" O GLYAD 216 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASNAD 218 " --> pdb=" O LEUAD 77 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ALAAD 79 " --> pdb=" O ASNAD 218 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALAAD 220 " --> pdb=" O ALAAD 79 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILEAD 81 " --> pdb=" O ALAAD 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 87 through 97 removed outlier: 8.126A pdb=" N LYS 3 155 " --> pdb=" O ASN 3 87 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN 3 89 " --> pdb=" O LYS 3 155 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN 3 157 " --> pdb=" O GLN 3 89 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASN 3 91 " --> pdb=" O ASN 3 157 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA 3 159 " --> pdb=" O ASN 3 91 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA 3 93 " --> pdb=" O ALA 3 159 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL 3 161 " --> pdb=" O ALA 3 93 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE 3 95 " --> pdb=" O VAL 3 161 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 155 through 161 current: chain '4' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 155 through 161 current: chain '5' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 155 through 161 current: chain '6' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 155 through 161 current: chain '7' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 155 through 161 current: chain '8' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain '8' and resid 155 through 161 current: chain '9' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain '9' and resid 155 through 161 current: chain '0' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 155 through 161 current: chain 'AA' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain 'AA' and resid 155 through 161 current: chain 'AB' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain 'AB' and resid 155 through 161 current: chain 'AC' and resid 155 through 161 WARNING: can't find start of bonding for strands! previous: chain 'AC' and resid 155 through 161 current: chain 'AD' and resid 155 through 161 No H-bonds generated for sheet with id=AA4 317 hydrogen bonds defined for protein. 843 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: 7.60 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 16368 1.13 - 1.30: 3356 1.30 - 1.48: 5783 1.48 - 1.65: 8225 1.65 - 1.82: 12 Bond restraints: 33744 Sorted by residual: bond pdb=" N ASPAB 57 " pdb=" CA ASPAB 57 " ideal model delta sigma weight residual 1.455 1.625 -0.171 1.25e-02 6.40e+03 1.86e+02 bond pdb=" N ASPAA 57 " pdb=" CA ASPAA 57 " ideal model delta sigma weight residual 1.455 1.625 -0.170 1.25e-02 6.40e+03 1.86e+02 bond pdb=" N ASP 7 57 " pdb=" CA ASP 7 57 " ideal model delta sigma weight residual 1.455 1.625 -0.170 1.25e-02 6.40e+03 1.86e+02 bond pdb=" N ASP 8 57 " pdb=" CA ASP 8 57 " ideal model delta sigma weight residual 1.455 1.625 -0.170 1.25e-02 6.40e+03 1.86e+02 bond pdb=" N ASP 3 57 " pdb=" CA ASP 3 57 " ideal model delta sigma weight residual 1.455 1.625 -0.170 1.25e-02 6.40e+03 1.85e+02 ... (remaining 33739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 49635 3.16 - 6.33: 8655 6.33 - 9.49: 1815 9.49 - 12.65: 257 12.65 - 15.81: 94 Bond angle restraints: 60456 Sorted by residual: angle pdb=" N LEU 9 205 " pdb=" CA LEU 9 205 " pdb=" C LEU 9 205 " ideal model delta sigma weight residual 111.92 126.58 -14.66 1.34e+00 5.57e-01 1.20e+02 angle pdb=" N LEUAD 205 " pdb=" CA LEUAD 205 " pdb=" C LEUAD 205 " ideal model delta sigma weight residual 111.92 126.58 -14.66 1.34e+00 5.57e-01 1.20e+02 angle pdb=" N LEU 3 205 " pdb=" CA LEU 3 205 " pdb=" C LEU 3 205 " ideal model delta sigma weight residual 111.92 126.57 -14.65 1.34e+00 5.57e-01 1.20e+02 angle pdb=" N LEUAB 205 " pdb=" CA LEUAB 205 " pdb=" C LEUAB 205 " ideal model delta sigma weight residual 111.92 126.57 -14.65 1.34e+00 5.57e-01 1.20e+02 angle pdb=" N LEU 8 205 " pdb=" CA LEU 8 205 " pdb=" C LEU 8 205 " ideal model delta sigma weight residual 111.92 126.57 -14.65 1.34e+00 5.57e-01 1.20e+02 ... (remaining 60451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13980 17.91 - 35.82: 1356 35.82 - 53.73: 384 53.73 - 71.64: 348 71.64 - 89.55: 72 Dihedral angle restraints: 16140 sinusoidal: 8784 harmonic: 7356 Sorted by residual: dihedral pdb=" C THR 4 60 " pdb=" N THR 4 60 " pdb=" CA THR 4 60 " pdb=" CB THR 4 60 " ideal model delta harmonic sigma weight residual -122.00 -139.70 17.70 0 2.50e+00 1.60e-01 5.01e+01 dihedral pdb=" C THR 5 60 " pdb=" N THR 5 60 " pdb=" CA THR 5 60 " pdb=" CB THR 5 60 " ideal model delta harmonic sigma weight residual -122.00 -139.69 17.69 0 2.50e+00 1.60e-01 5.01e+01 dihedral pdb=" C THRAC 60 " pdb=" N THRAC 60 " pdb=" CA THRAC 60 " pdb=" CB THRAC 60 " ideal model delta harmonic sigma weight residual -122.00 -139.68 17.68 0 2.50e+00 1.60e-01 5.00e+01 ... (remaining 16137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1870 0.123 - 0.246: 710 0.246 - 0.369: 72 0.369 - 0.492: 60 0.492 - 0.615: 60 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CA ASNAB 132 " pdb=" N ASNAB 132 " pdb=" C ASNAB 132 " pdb=" CB ASNAB 132 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.62 2.00e-01 2.50e+01 9.46e+00 chirality pdb=" CA ASN 5 132 " pdb=" N ASN 5 132 " pdb=" C ASN 5 132 " pdb=" CB ASN 5 132 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" CA ASN 4 132 " pdb=" N ASN 4 132 " pdb=" C ASN 4 132 " pdb=" CB ASN 4 132 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.42e+00 ... (remaining 2769 not shown) Planarity restraints: 5724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN 6 48 " 0.141 2.00e-02 2.50e+03 1.44e-01 3.09e+02 pdb=" CD GLN 6 48 " -0.060 2.00e-02 2.50e+03 pdb=" OE1 GLN 6 48 " -0.071 2.00e-02 2.50e+03 pdb=" NE2 GLN 6 48 " -0.176 2.00e-02 2.50e+03 pdb="HE21 GLN 6 48 " -0.076 2.00e-02 2.50e+03 pdb="HE22 GLN 6 48 " 0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN 3 48 " 0.141 2.00e-02 2.50e+03 1.44e-01 3.09e+02 pdb=" CD GLN 3 48 " -0.059 2.00e-02 2.50e+03 pdb=" OE1 GLN 3 48 " -0.071 2.00e-02 2.50e+03 pdb=" NE2 GLN 3 48 " -0.176 2.00e-02 2.50e+03 pdb="HE21 GLN 3 48 " -0.076 2.00e-02 2.50e+03 pdb="HE22 GLN 3 48 " 0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN 8 48 " 0.141 2.00e-02 2.50e+03 1.44e-01 3.09e+02 pdb=" CD GLN 8 48 " -0.059 2.00e-02 2.50e+03 pdb=" OE1 GLN 8 48 " -0.071 2.00e-02 2.50e+03 pdb=" NE2 GLN 8 48 " -0.176 2.00e-02 2.50e+03 pdb="HE21 GLN 8 48 " -0.076 2.00e-02 2.50e+03 pdb="HE22 GLN 8 48 " 0.242 2.00e-02 2.50e+03 ... (remaining 5721 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 4974 2.25 - 2.84: 66553 2.84 - 3.42: 94583 3.42 - 4.01: 125859 4.01 - 4.60: 183290 Nonbonded interactions: 475259 Sorted by model distance: nonbonded pdb=" HG1 THRAB 96 " pdb=" O ALAAB 163 " model vdw 1.662 2.450 nonbonded pdb=" HG1 THR 9 96 " pdb=" O ALA 9 163 " model vdw 1.662 2.450 nonbonded pdb=" HG1 THR 6 96 " pdb=" O ALA 6 163 " model vdw 1.662 2.450 nonbonded pdb=" HG1 THR 0 96 " pdb=" O ALA 0 163 " model vdw 1.662 2.450 nonbonded pdb=" HG1 THR 7 96 " pdb=" O ALA 7 163 " model vdw 1.662 2.450 ... (remaining 475254 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: 0.05 Found NCS groups: ncs_group { reference = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain '0' selection = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' } 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: 1.840 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: 0.200 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 26.590 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3399 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 : 0.016 0.171 17364 Z= 1.197 Angle : 2.961 15.813 23604 Z= 1.982 Chirality : 0.152 0.615 2772 Planarity : 0.012 0.046 3300 Dihedral : 17.390 89.549 5976 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Cbeta Deviations : 3.26 % 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 aren not related in a simple way. whole: -4.31 (0.12), residues: 2436 helix: -5.36 (0.11), residues: 84 sheet: -1.29 (0.20), residues: 552 loop : -3.57 (0.09), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.007 TYRAB 112 PHE 0.028 0.013 PHEAA 183 HIS 0.007 0.004 HISAD 182 Details of bonding type rmsd covalent geometry : bond 0.01645 (17364) covalent geometry : angle 2.96138 (23604) hydrogen bonds : bond 0.18242 ( 317) hydrogen bonds : angle 12.06873 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.781 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 4 80 ASN cc_start: 0.6540 (m110) cc_final: 0.6254 (m-40) REVERT: 5 80 ASN cc_start: 0.6605 (m110) cc_final: 0.6096 (m-40) REVERT: 9 132 ASN cc_start: 0.8007 (p0) cc_final: 0.7787 (p0) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.2460 time to fit residues: 148.2277 Evaluate side-chains 285 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 173 ASN 3 196 GLN ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 ASN ** 4 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 182 HIS 4 185 ASN ** 5 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 182 HIS 5 185 ASN ** 5 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 80 ASN 6 91 ASN 6 182 HIS 7 80 ASN 7 91 ASN 7 136 ASN 7 145 ASN 8 91 ASN ** 8 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 91 ASN 9 136 ASN 9 182 HIS 9 196 GLN 0 91 ASN ** 0 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 182 HIS 0 196 GLN AA 91 ASN AA 182 HIS AB 91 ASN AB 182 HIS AC 80 ASN ** AC 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 185 ASN ** AD 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6927 r_free = 0.6927 target = 0.439135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.6884 r_free = 0.6884 target = 0.351976 restraints weight = 154829.064| |-----------------------------------------------------------------------------| r_work (start): 0.6529 rms_B_bonded: 12.98 r_work: 0.7542 rms_B_bonded: 7.01 restraints_weight: 2.0000 r_work (final): 0.7542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 17364 Z= 0.367 Angle : 1.158 8.144 23604 Z= 0.672 Chirality : 0.062 0.214 2772 Planarity : 0.005 0.050 3300 Dihedral : 13.220 46.185 2484 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 29.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.78 % Favored : 85.14 % Rotamer: Outliers : 3.31 % Allowed : 11.20 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.96 % 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 aren not related in a simple way. whole: -5.40 (0.12), residues: 2436 helix: -5.38 (0.11), residues: 84 sheet: -3.27 (0.15), residues: 840 loop : -3.85 (0.09), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR 6 112 PHE 0.020 0.003 PHE 6 106 HIS 0.010 0.002 HIS 5 182 Details of bonding type rmsd covalent geometry : bond 0.00672 (17364) covalent geometry : angle 1.15787 (23604) hydrogen bonds : bond 0.04938 ( 317) hydrogen bonds : angle 9.54040 ( 843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 338 time to evaluate : 0.807 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 4 184 LEU cc_start: 0.8292 (tp) cc_final: 0.8006 (tp) REVERT: 5 218 ASN cc_start: 0.6538 (OUTLIER) cc_final: 0.5404 (p0) REVERT: 0 52 ASP cc_start: 0.3240 (OUTLIER) cc_final: 0.2967 (p0) REVERT: AC 52 ASP cc_start: 0.3528 (OUTLIER) cc_final: 0.3027 (p0) REVERT: AD 133 ASN cc_start: 0.7747 (t0) cc_final: 0.7544 (t0) outliers start: 60 outliers final: 42 residues processed: 384 average time/residue: 0.2395 time to fit residues: 145.8900 Evaluate side-chains 325 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 280 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 47 THR Chi-restraints excluded: chain 3 residue 73 SER Chi-restraints excluded: chain 3 residue 88 GLN Chi-restraints excluded: chain 3 residue 91 ASN Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 88 GLN Chi-restraints excluded: chain 4 residue 152 ASN Chi-restraints excluded: chain 4 residue 217 VAL Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 88 GLN Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 176 GLN Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 218 ASN Chi-restraints excluded: chain 6 residue 52 ASP Chi-restraints excluded: chain 6 residue 176 GLN Chi-restraints excluded: chain 6 residue 217 VAL Chi-restraints excluded: chain 6 residue 237 CYS Chi-restraints excluded: chain 7 residue 52 ASP Chi-restraints excluded: chain 7 residue 204 LEU Chi-restraints excluded: chain 7 residue 215 ILE Chi-restraints excluded: chain 7 residue 217 VAL Chi-restraints excluded: chain 8 residue 52 ASP Chi-restraints excluded: chain 8 residue 176 GLN Chi-restraints excluded: chain 8 residue 204 LEU Chi-restraints excluded: chain 8 residue 217 VAL Chi-restraints excluded: chain 9 residue 146 VAL Chi-restraints excluded: chain 9 residue 182 HIS Chi-restraints excluded: chain 9 residue 204 LEU Chi-restraints excluded: chain 9 residue 217 VAL Chi-restraints excluded: chain 0 residue 52 ASP Chi-restraints excluded: chain 0 residue 176 GLN Chi-restraints excluded: chain 0 residue 182 HIS Chi-restraints excluded: chain 0 residue 204 LEU Chi-restraints excluded: chain AA residue 176 GLN Chi-restraints excluded: chain AA residue 182 HIS Chi-restraints excluded: chain AA residue 204 LEU Chi-restraints excluded: chain AB residue 70 LEU Chi-restraints excluded: chain AB residue 176 GLN Chi-restraints excluded: chain AB residue 182 HIS Chi-restraints excluded: chain AC residue 52 ASP Chi-restraints excluded: chain AC residue 176 GLN Chi-restraints excluded: chain AD residue 176 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 64 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 232 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 126 GLN ** 3 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 209 ASN ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 80 ASN ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 80 ASN 5 91 ASN ** 5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 157 ASN 7 176 GLN 8 157 ASN ** 8 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 157 ASN ** 9 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 157 ASN ** 0 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 80 ASN AD 153 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6562 r_free = 0.6562 target = 0.432245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.7122 r_free = 0.7122 target = 0.313821 restraints weight = 116061.999| |-----------------------------------------------------------------------------| r_work (start): 0.6455 rms_B_bonded: 10.96 r_work: 0.7700 rms_B_bonded: 5.65 restraints_weight: 2.0000 r_work (final): 0.7700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17364 Z= 0.294 Angle : 1.034 8.947 23604 Z= 0.594 Chirality : 0.056 0.232 2772 Planarity : 0.004 0.052 3300 Dihedral : 12.162 41.538 2484 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 32.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.49 % Favored : 82.51 % Rotamer: Outliers : 5.57 % Allowed : 14.40 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.90 % 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 aren not related in a simple way. whole: -5.83 (0.11), residues: 2436 helix: -5.37 (0.11), residues: 84 sheet: -3.50 (0.15), residues: 864 loop : -4.22 (0.09), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR 7 112 PHE 0.019 0.003 PHE 0 55 HIS 0.025 0.003 HIS 0 182 Details of bonding type rmsd covalent geometry : bond 0.00532 (17364) covalent geometry : angle 1.03434 (23604) hydrogen bonds : bond 0.03899 ( 317) hydrogen bonds : angle 8.80927 ( 843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 306 time to evaluate : 0.825 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 218 ASN cc_start: 0.6278 (OUTLIER) cc_final: 0.5699 (p0) REVERT: 8 145 ASN cc_start: 0.7274 (OUTLIER) cc_final: 0.6958 (m-40) REVERT: 9 145 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.6786 (m-40) REVERT: AC 52 ASP cc_start: 0.3662 (OUTLIER) cc_final: 0.2923 (p0) REVERT: AD 227 GLN cc_start: 0.6508 (mp10) cc_final: 0.6196 (mt0) outliers start: 101 outliers final: 73 residues processed: 390 average time/residue: 0.2676 time to fit residues: 167.5550 Evaluate side-chains 335 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 52 ASP Chi-restraints excluded: chain 3 residue 73 SER Chi-restraints excluded: chain 3 residue 88 GLN Chi-restraints excluded: chain 3 residue 136 ASN Chi-restraints excluded: chain 4 residue 73 SER Chi-restraints excluded: chain 4 residue 88 GLN Chi-restraints excluded: chain 4 residue 146 VAL Chi-restraints excluded: chain 4 residue 152 ASN Chi-restraints excluded: chain 4 residue 217 VAL Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 5 residue 69 SER Chi-restraints excluded: chain 5 residue 88 GLN Chi-restraints excluded: chain 5 residue 145 ASN Chi-restraints excluded: chain 5 residue 146 VAL Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 176 GLN Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 218 ASN Chi-restraints excluded: chain 6 residue 69 SER Chi-restraints excluded: chain 6 residue 73 SER Chi-restraints excluded: chain 6 residue 110 ASP Chi-restraints excluded: chain 6 residue 146 VAL Chi-restraints excluded: chain 6 residue 176 GLN Chi-restraints excluded: chain 6 residue 179 LEU Chi-restraints excluded: chain 6 residue 217 VAL Chi-restraints excluded: chain 7 residue 52 ASP Chi-restraints excluded: chain 7 residue 69 SER Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 110 ASP Chi-restraints excluded: chain 7 residue 146 VAL Chi-restraints excluded: chain 7 residue 179 LEU Chi-restraints excluded: chain 8 residue 69 SER Chi-restraints excluded: chain 8 residue 73 SER Chi-restraints excluded: chain 8 residue 87 ASN Chi-restraints excluded: chain 8 residue 145 ASN Chi-restraints excluded: chain 8 residue 146 VAL Chi-restraints excluded: chain 8 residue 152 ASN Chi-restraints excluded: chain 8 residue 153 GLN Chi-restraints excluded: chain 8 residue 176 GLN Chi-restraints excluded: chain 8 residue 179 LEU Chi-restraints excluded: chain 8 residue 215 ILE Chi-restraints excluded: chain 8 residue 225 ASN Chi-restraints excluded: chain 9 residue 52 ASP Chi-restraints excluded: chain 9 residue 73 SER Chi-restraints excluded: chain 9 residue 87 ASN Chi-restraints excluded: chain 9 residue 145 ASN Chi-restraints excluded: chain 9 residue 146 VAL Chi-restraints excluded: chain 9 residue 179 LEU Chi-restraints excluded: chain 9 residue 215 ILE Chi-restraints excluded: chain 9 residue 225 ASN Chi-restraints excluded: chain 0 residue 52 ASP Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 87 ASN Chi-restraints excluded: chain 0 residue 145 ASN Chi-restraints excluded: chain 0 residue 146 VAL Chi-restraints excluded: chain 0 residue 176 GLN Chi-restraints excluded: chain 0 residue 179 LEU Chi-restraints excluded: chain 0 residue 225 ASN Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 87 ASN Chi-restraints excluded: chain AA residue 88 GLN Chi-restraints excluded: chain AA residue 176 GLN Chi-restraints excluded: chain AA residue 179 LEU Chi-restraints excluded: chain AA residue 225 ASN Chi-restraints excluded: chain AB residue 87 ASN Chi-restraints excluded: chain AB residue 146 VAL Chi-restraints excluded: chain AB residue 153 GLN Chi-restraints excluded: chain AB residue 176 GLN Chi-restraints excluded: chain AB residue 179 LEU Chi-restraints excluded: chain AB residue 225 ASN Chi-restraints excluded: chain AC residue 52 ASP Chi-restraints excluded: chain AC residue 153 GLN Chi-restraints excluded: chain AC residue 176 GLN Chi-restraints excluded: chain AC residue 179 LEU Chi-restraints excluded: chain AD residue 176 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 140 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 215 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 150 GLN ** 3 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 225 ASN ** 6 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 209 ASN ** 7 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 209 ASN ** 9 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 182 HIS 0 209 ASN ** 0 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 209 ASN ** AA 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 181 ASN ** AB 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 145 ASN AD 181 ASN AD 182 HIS ** AD 225 ASN ** 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 = 0.6888 r_free = 0.6888 target = 0.432424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.6846 r_free = 0.6846 target = 0.337745 restraints weight = 149674.381| |-----------------------------------------------------------------------------| r_work (start): 0.6463 rms_B_bonded: 13.07 r_work: 0.7541 rms_B_bonded: 6.79 restraints_weight: 2.0000 r_work (final): 0.7541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.7251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17364 Z= 0.278 Angle : 0.982 8.524 23604 Z= 0.558 Chirality : 0.054 0.205 2772 Planarity : 0.004 0.052 3300 Dihedral : 11.580 40.944 2484 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 34.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.70 % Favored : 80.30 % Rotamer: Outliers : 6.02 % Allowed : 16.83 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.90 % 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 aren not related in a simple way. whole: -6.36 (0.11), residues: 2436 helix: -5.36 (0.11), residues: 84 sheet: -4.20 (0.15), residues: 780 loop : -4.41 (0.08), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR 7 112 PHE 0.020 0.003 PHEAB 183 HIS 0.007 0.001 HIS 0 182 Details of bonding type rmsd covalent geometry : bond 0.00530 (17364) covalent geometry : angle 0.98167 (23604) hydrogen bonds : bond 0.03966 ( 317) hydrogen bonds : angle 8.27803 ( 843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 270 time to evaluate : 1.056 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: 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: 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: 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: 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: 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: 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: 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: 5 136 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6926 (m-40) REVERT: 8 145 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.7104 (m-40) REVERT: 9 145 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7078 (m-40) REVERT: 0 97 SER cc_start: 0.7329 (t) cc_final: 0.7082 (p) REVERT: AC 52 ASP cc_start: 0.3182 (OUTLIER) cc_final: 0.1702 (p0) REVERT: AC 119 LYS cc_start: 0.7307 (mttp) cc_final: 0.6967 (mmtm) REVERT: AD 176 GLN cc_start: -0.1872 (OUTLIER) cc_final: -0.2656 (mt0) REVERT: AD 205 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6786 (mm) REVERT: AD 227 GLN cc_start: 0.6717 (mp10) cc_final: 0.5592 (mt0) outliers start: 109 outliers final: 85 residues processed: 362 average time/residue: 0.2347 time to fit residues: 136.6318 Evaluate side-chains 336 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 245 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 3 residue 52 ASP Chi-restraints excluded: chain 3 residue 73 SER Chi-restraints excluded: chain 3 residue 88 GLN Chi-restraints excluded: chain 3 residue 145 ASN Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 225 ASN Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 73 SER Chi-restraints excluded: chain 4 residue 88 GLN Chi-restraints excluded: chain 4 residue 145 ASN Chi-restraints excluded: chain 4 residue 146 VAL Chi-restraints excluded: chain 4 residue 152 ASN Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 217 VAL Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 4 residue 233 LEU Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 73 SER Chi-restraints excluded: chain 5 residue 88 GLN Chi-restraints excluded: chain 5 residue 136 ASN Chi-restraints excluded: chain 5 residue 145 ASN Chi-restraints excluded: chain 5 residue 146 VAL Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 176 GLN Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 215 ILE Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 225 ASN Chi-restraints excluded: chain 5 residue 233 LEU Chi-restraints excluded: chain 6 residue 52 ASP Chi-restraints excluded: chain 6 residue 69 SER Chi-restraints excluded: chain 6 residue 73 SER Chi-restraints excluded: chain 6 residue 87 ASN Chi-restraints excluded: chain 6 residue 110 ASP Chi-restraints excluded: chain 6 residue 136 ASN Chi-restraints excluded: chain 6 residue 146 VAL Chi-restraints excluded: chain 6 residue 176 GLN Chi-restraints excluded: chain 7 residue 52 ASP Chi-restraints excluded: chain 7 residue 69 SER Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 146 VAL Chi-restraints excluded: chain 7 residue 152 ASN Chi-restraints excluded: chain 7 residue 215 ILE Chi-restraints excluded: chain 8 residue 52 ASP Chi-restraints excluded: chain 8 residue 69 SER Chi-restraints excluded: chain 8 residue 73 SER Chi-restraints excluded: chain 8 residue 87 ASN Chi-restraints excluded: chain 8 residue 145 ASN Chi-restraints excluded: chain 8 residue 146 VAL Chi-restraints excluded: chain 8 residue 152 ASN Chi-restraints excluded: chain 8 residue 176 GLN Chi-restraints excluded: chain 8 residue 225 ASN Chi-restraints excluded: chain 9 residue 52 ASP Chi-restraints excluded: chain 9 residue 73 SER Chi-restraints excluded: chain 9 residue 87 ASN Chi-restraints excluded: chain 9 residue 145 ASN Chi-restraints excluded: chain 9 residue 146 VAL Chi-restraints excluded: chain 9 residue 152 ASN Chi-restraints excluded: chain 9 residue 215 ILE Chi-restraints excluded: chain 9 residue 225 ASN Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 87 ASN Chi-restraints excluded: chain 0 residue 146 VAL Chi-restraints excluded: chain 0 residue 176 GLN Chi-restraints excluded: chain 0 residue 215 ILE Chi-restraints excluded: chain 0 residue 225 ASN Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 73 SER Chi-restraints excluded: chain AA residue 87 ASN Chi-restraints excluded: chain AA residue 88 GLN Chi-restraints excluded: chain AA residue 146 VAL Chi-restraints excluded: chain AA residue 160 ILE Chi-restraints excluded: chain AA residue 176 GLN Chi-restraints excluded: chain AA residue 215 ILE Chi-restraints excluded: chain AA residue 225 ASN Chi-restraints excluded: chain AB residue 52 ASP Chi-restraints excluded: chain AB residue 73 SER Chi-restraints excluded: chain AB residue 87 ASN Chi-restraints excluded: chain AB residue 146 VAL Chi-restraints excluded: chain AB residue 160 ILE Chi-restraints excluded: chain AB residue 176 GLN Chi-restraints excluded: chain AB residue 225 ASN Chi-restraints excluded: chain AC residue 52 ASP Chi-restraints excluded: chain AC residue 87 ASN Chi-restraints excluded: chain AC residue 153 GLN Chi-restraints excluded: chain AC residue 176 GLN Chi-restraints excluded: chain AD residue 176 GLN Chi-restraints excluded: chain AD residue 205 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 197 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 185 ASN ** 9 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 181 ASN 0 206 ASN 0 209 ASN ** 0 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 200 ASN AA 206 ASN AA 209 ASN ** AA 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 173 ASN ** AB 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 156 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6906 r_free = 0.6906 target = 0.434330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.7740 r_free = 0.7740 target = 0.314999 restraints weight = 151044.727| |-----------------------------------------------------------------------------| r_work (start): 0.6445 rms_B_bonded: 12.48 r_work: 0.7666 rms_B_bonded: 6.35 restraints_weight: 2.0000 r_work (final): 0.7666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.7595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17364 Z= 0.211 Angle : 0.914 8.044 23604 Z= 0.520 Chirality : 0.051 0.168 2772 Planarity : 0.004 0.058 3300 Dihedral : 10.939 38.591 2484 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.51 % Favored : 81.49 % Rotamer: Outliers : 5.46 % Allowed : 18.60 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.44 % 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 aren not related in a simple way. whole: -6.31 (0.11), residues: 2436 helix: -5.36 (0.11), residues: 84 sheet: -4.04 (0.16), residues: 708 loop : -4.49 (0.08), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR 9 112 PHE 0.018 0.002 PHE 8 183 HIS 0.002 0.001 HIS 9 182 Details of bonding type rmsd covalent geometry : bond 0.00390 (17364) covalent geometry : angle 0.91415 (23604) hydrogen bonds : bond 0.03194 ( 317) hydrogen bonds : angle 7.78595 ( 843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 255 time to evaluate : 0.879 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 136 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6729 (m-40) REVERT: 8 145 ASN cc_start: 0.7068 (OUTLIER) cc_final: 0.6654 (m-40) REVERT: 9 145 ASN cc_start: 0.7059 (OUTLIER) cc_final: 0.6370 (m-40) REVERT: AC 52 ASP cc_start: 0.3036 (OUTLIER) cc_final: 0.2240 (p0) REVERT: AD 176 GLN cc_start: -0.1912 (OUTLIER) cc_final: -0.2730 (mt0) REVERT: AD 227 GLN cc_start: 0.6612 (mp10) cc_final: 0.5372 (mt0) outliers start: 99 outliers final: 75 residues processed: 342 average time/residue: 0.2494 time to fit residues: 137.3466 Evaluate side-chains 321 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 241 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 52 ASP Chi-restraints excluded: chain 3 residue 73 SER Chi-restraints excluded: chain 3 residue 145 ASN Chi-restraints excluded: chain 3 residue 152 ASN Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 73 SER Chi-restraints excluded: chain 4 residue 80 ASN Chi-restraints excluded: chain 4 residue 88 GLN Chi-restraints excluded: chain 4 residue 96 THR Chi-restraints excluded: chain 4 residue 145 ASN Chi-restraints excluded: chain 4 residue 146 VAL Chi-restraints excluded: chain 4 residue 152 ASN Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 217 VAL Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 73 SER Chi-restraints excluded: chain 5 residue 80 ASN Chi-restraints excluded: chain 5 residue 96 THR Chi-restraints excluded: chain 5 residue 136 ASN Chi-restraints excluded: chain 5 residue 145 ASN Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 6 residue 52 ASP Chi-restraints excluded: chain 6 residue 69 SER Chi-restraints excluded: chain 6 residue 73 SER Chi-restraints excluded: chain 6 residue 133 ASN Chi-restraints excluded: chain 6 residue 146 VAL Chi-restraints excluded: chain 6 residue 176 GLN Chi-restraints excluded: chain 7 residue 69 SER Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 146 VAL Chi-restraints excluded: chain 7 residue 152 ASN Chi-restraints excluded: chain 7 residue 215 ILE Chi-restraints excluded: chain 8 residue 52 ASP Chi-restraints excluded: chain 8 residue 69 SER Chi-restraints excluded: chain 8 residue 73 SER Chi-restraints excluded: chain 8 residue 87 ASN Chi-restraints excluded: chain 8 residue 145 ASN Chi-restraints excluded: chain 8 residue 146 VAL Chi-restraints excluded: chain 8 residue 152 ASN Chi-restraints excluded: chain 8 residue 176 GLN Chi-restraints excluded: chain 9 residue 52 ASP Chi-restraints excluded: chain 9 residue 69 SER Chi-restraints excluded: chain 9 residue 87 ASN Chi-restraints excluded: chain 9 residue 145 ASN Chi-restraints excluded: chain 9 residue 146 VAL Chi-restraints excluded: chain 9 residue 215 ILE Chi-restraints excluded: chain 9 residue 225 ASN Chi-restraints excluded: chain 0 residue 87 ASN Chi-restraints excluded: chain 0 residue 145 ASN Chi-restraints excluded: chain 0 residue 176 GLN Chi-restraints excluded: chain 0 residue 206 ASN Chi-restraints excluded: chain 0 residue 215 ILE Chi-restraints excluded: chain 0 residue 225 ASN Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 87 ASN Chi-restraints excluded: chain AA residue 88 GLN Chi-restraints excluded: chain AA residue 146 VAL Chi-restraints excluded: chain AA residue 160 ILE Chi-restraints excluded: chain AA residue 176 GLN Chi-restraints excluded: chain AA residue 206 ASN Chi-restraints excluded: chain AA residue 215 ILE Chi-restraints excluded: chain AB residue 52 ASP Chi-restraints excluded: chain AB residue 87 ASN Chi-restraints excluded: chain AB residue 145 ASN Chi-restraints excluded: chain AB residue 146 VAL Chi-restraints excluded: chain AB residue 176 GLN Chi-restraints excluded: chain AB residue 225 ASN Chi-restraints excluded: chain AC residue 52 ASP Chi-restraints excluded: chain AC residue 87 ASN Chi-restraints excluded: chain AC residue 146 VAL Chi-restraints excluded: chain AC residue 152 ASN Chi-restraints excluded: chain AC residue 153 GLN Chi-restraints excluded: chain AC residue 176 GLN Chi-restraints excluded: chain AD residue 176 GLN Chi-restraints excluded: chain AD residue 205 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 157 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 225 ASN ** 6 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 185 ASN 8 196 GLN 8 206 ASN 8 209 ASN 8 225 ASN 9 225 ASN 0 185 ASN 0 206 ASN 0 209 ASN ** 0 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 157 ASN AA 181 ASN ** AA 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 173 ASN AB 209 ASN ** AB 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6888 r_free = 0.6888 target = 0.430475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.7498 r_free = 0.7498 target = 0.311615 restraints weight = 149074.331| |-----------------------------------------------------------------------------| r_work (start): 0.6401 rms_B_bonded: 13.93 r_work: 0.7533 rms_B_bonded: 6.89 restraints_weight: 2.0000 r_work (final): 0.7533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.8315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 17364 Z= 0.279 Angle : 0.954 9.092 23604 Z= 0.538 Chirality : 0.053 0.240 2772 Planarity : 0.004 0.054 3300 Dihedral : 11.112 43.490 2484 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 36.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 21.55 % Favored : 78.37 % Rotamer: Outliers : 6.40 % Allowed : 18.38 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.57 % 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 aren not related in a simple way. whole: -6.59 (0.09), residues: 2436 helix: -5.35 (0.11), residues: 84 sheet: -4.84 (0.16), residues: 492 loop : -4.60 (0.07), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR 9 112 PHE 0.015 0.002 PHE 0 55 HIS 0.004 0.001 HISAC 182 Details of bonding type rmsd covalent geometry : bond 0.00523 (17364) covalent geometry : angle 0.95407 (23604) hydrogen bonds : bond 0.03865 ( 317) hydrogen bonds : angle 8.00445 ( 843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 241 time to evaluate : 0.620 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: 6 229 ASN cc_start: 0.8160 (t0) cc_final: 0.6936 (t0) REVERT: 8 145 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7238 (m-40) REVERT: AA 133 ASN cc_start: 0.7117 (t0) cc_final: 0.5569 (t0) REVERT: AC 52 ASP cc_start: 0.3276 (OUTLIER) cc_final: 0.2400 (p0) REVERT: AD 67 ASN cc_start: 0.5439 (t0) cc_final: 0.5075 (t0) outliers start: 116 outliers final: 96 residues processed: 339 average time/residue: 0.2205 time to fit residues: 121.2088 Evaluate side-chains 325 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 227 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 3 residue 52 ASP Chi-restraints excluded: chain 3 residue 73 SER Chi-restraints excluded: chain 3 residue 88 GLN Chi-restraints excluded: chain 3 residue 145 ASN Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 152 ASN Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 73 SER Chi-restraints excluded: chain 4 residue 88 GLN Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 145 ASN Chi-restraints excluded: chain 4 residue 146 VAL Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 217 VAL Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 69 SER Chi-restraints excluded: chain 5 residue 73 SER Chi-restraints excluded: chain 5 residue 80 ASN Chi-restraints excluded: chain 5 residue 110 ASP Chi-restraints excluded: chain 5 residue 136 ASN Chi-restraints excluded: chain 5 residue 145 ASN Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 160 ILE Chi-restraints excluded: chain 5 residue 215 ILE Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 225 ASN Chi-restraints excluded: chain 6 residue 52 ASP Chi-restraints excluded: chain 6 residue 69 SER Chi-restraints excluded: chain 6 residue 73 SER Chi-restraints excluded: chain 6 residue 87 ASN Chi-restraints excluded: chain 6 residue 133 ASN Chi-restraints excluded: chain 6 residue 146 VAL Chi-restraints excluded: chain 7 residue 69 SER Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 146 VAL Chi-restraints excluded: chain 7 residue 152 ASN Chi-restraints excluded: chain 7 residue 215 ILE Chi-restraints excluded: chain 8 residue 52 ASP Chi-restraints excluded: chain 8 residue 69 SER Chi-restraints excluded: chain 8 residue 73 SER Chi-restraints excluded: chain 8 residue 87 ASN Chi-restraints excluded: chain 8 residue 145 ASN Chi-restraints excluded: chain 8 residue 146 VAL Chi-restraints excluded: chain 8 residue 152 ASN Chi-restraints excluded: chain 8 residue 153 GLN Chi-restraints excluded: chain 8 residue 176 GLN Chi-restraints excluded: chain 9 residue 52 ASP Chi-restraints excluded: chain 9 residue 69 SER Chi-restraints excluded: chain 9 residue 73 SER Chi-restraints excluded: chain 9 residue 87 ASN Chi-restraints excluded: chain 9 residue 131 LEU Chi-restraints excluded: chain 9 residue 145 ASN Chi-restraints excluded: chain 9 residue 146 VAL Chi-restraints excluded: chain 9 residue 215 ILE Chi-restraints excluded: chain 9 residue 225 ASN Chi-restraints excluded: chain 9 residue 232 THR Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 77 LEU Chi-restraints excluded: chain 0 residue 87 ASN Chi-restraints excluded: chain 0 residue 131 LEU Chi-restraints excluded: chain 0 residue 133 ASN Chi-restraints excluded: chain 0 residue 145 ASN Chi-restraints excluded: chain 0 residue 146 VAL Chi-restraints excluded: chain 0 residue 176 GLN Chi-restraints excluded: chain 0 residue 215 ILE Chi-restraints excluded: chain 0 residue 225 ASN Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 73 SER Chi-restraints excluded: chain AA residue 77 LEU Chi-restraints excluded: chain AA residue 87 ASN Chi-restraints excluded: chain AA residue 146 VAL Chi-restraints excluded: chain AA residue 176 GLN Chi-restraints excluded: chain AA residue 215 ILE Chi-restraints excluded: chain AA residue 225 ASN Chi-restraints excluded: chain AA residue 231 LEU Chi-restraints excluded: chain AB residue 52 ASP Chi-restraints excluded: chain AB residue 73 SER Chi-restraints excluded: chain AB residue 87 ASN Chi-restraints excluded: chain AB residue 145 ASN Chi-restraints excluded: chain AB residue 146 VAL Chi-restraints excluded: chain AB residue 176 GLN Chi-restraints excluded: chain AB residue 215 ILE Chi-restraints excluded: chain AB residue 225 ASN Chi-restraints excluded: chain AC residue 52 ASP Chi-restraints excluded: chain AC residue 87 ASN Chi-restraints excluded: chain AC residue 146 VAL Chi-restraints excluded: chain AC residue 152 ASN Chi-restraints excluded: chain AC residue 153 GLN Chi-restraints excluded: chain AC residue 176 GLN Chi-restraints excluded: chain AC residue 225 ASN Chi-restraints excluded: chain AD residue 87 ASN Chi-restraints excluded: chain AD residue 176 GLN Chi-restraints excluded: chain AD residue 225 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 0.0040 chunk 26 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 209 ASN ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 181 ASN ** 8 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 118 ASN ** 0 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 206 ASN AA 209 ASN ** AA 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 173 ASN ** AB 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 182 HIS ** AD 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 152 ASN ** 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 = 0.6916 r_free = 0.6916 target = 0.435689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.8403 r_free = 0.8403 target = 0.313476 restraints weight = 152296.889| |-----------------------------------------------------------------------------| r_work (start): 0.6424 rms_B_bonded: 10.37 r_work: 0.7858 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.7858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.8443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17364 Z= 0.172 Angle : 0.869 7.889 23604 Z= 0.494 Chirality : 0.050 0.169 2772 Planarity : 0.003 0.048 3300 Dihedral : 10.336 37.768 2484 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 26.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.63 % Favored : 83.29 % Rotamer: Outliers : 4.86 % Allowed : 19.81 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.03 % 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 aren not related in a simple way. whole: -6.26 (0.09), residues: 2436 helix: -5.35 (0.11), residues: 84 sheet: -4.21 (0.25), residues: 252 loop : -4.60 (0.07), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR 9 112 PHE 0.017 0.002 PHE 9 183 HIS 0.001 0.000 HISAD 182 Details of bonding type rmsd covalent geometry : bond 0.00322 (17364) covalent geometry : angle 0.86902 (23604) hydrogen bonds : bond 0.02885 ( 317) hydrogen bonds : angle 7.40615 ( 843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 248 time to evaluate : 0.741 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: 3 237 CYS cc_start: 0.6688 (p) cc_final: 0.6410 (t) REVERT: 6 81 ILE cc_start: 0.6607 (mm) cc_final: 0.6293 (mm) REVERT: 8 184 LEU cc_start: 0.9069 (tp) cc_final: 0.8814 (tp) REVERT: AC 52 ASP cc_start: 0.2860 (OUTLIER) cc_final: 0.2094 (p0) REVERT: AD 168 VAL cc_start: 0.3255 (t) cc_final: 0.3000 (m) REVERT: AD 227 GLN cc_start: 0.6590 (mp10) cc_final: 0.6215 (mt0) outliers start: 88 outliers final: 76 residues processed: 324 average time/residue: 0.2066 time to fit residues: 108.5712 Evaluate side-chains 311 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 234 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 3 residue 52 ASP Chi-restraints excluded: chain 3 residue 73 SER Chi-restraints excluded: chain 3 residue 88 GLN Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 152 ASN Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 73 SER Chi-restraints excluded: chain 4 residue 88 GLN Chi-restraints excluded: chain 4 residue 96 THR Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 145 ASN Chi-restraints excluded: chain 4 residue 152 ASN Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 217 VAL Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 73 SER Chi-restraints excluded: chain 5 residue 80 ASN Chi-restraints excluded: chain 5 residue 96 THR Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 215 ILE Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 225 ASN Chi-restraints excluded: chain 6 residue 52 ASP Chi-restraints excluded: chain 6 residue 69 SER Chi-restraints excluded: chain 6 residue 73 SER Chi-restraints excluded: chain 6 residue 133 ASN Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 125 THR Chi-restraints excluded: chain 7 residue 145 ASN Chi-restraints excluded: chain 7 residue 146 VAL Chi-restraints excluded: chain 7 residue 152 ASN Chi-restraints excluded: chain 7 residue 215 ILE Chi-restraints excluded: chain 8 residue 52 ASP Chi-restraints excluded: chain 8 residue 69 SER Chi-restraints excluded: chain 8 residue 87 ASN Chi-restraints excluded: chain 8 residue 131 LEU Chi-restraints excluded: chain 8 residue 145 ASN Chi-restraints excluded: chain 8 residue 146 VAL Chi-restraints excluded: chain 8 residue 152 ASN Chi-restraints excluded: chain 8 residue 153 GLN Chi-restraints excluded: chain 8 residue 176 GLN Chi-restraints excluded: chain 9 residue 52 ASP Chi-restraints excluded: chain 9 residue 69 SER Chi-restraints excluded: chain 9 residue 87 ASN Chi-restraints excluded: chain 9 residue 145 ASN Chi-restraints excluded: chain 9 residue 215 ILE Chi-restraints excluded: chain 9 residue 225 ASN Chi-restraints excluded: chain 9 residue 232 THR Chi-restraints excluded: chain 0 residue 69 SER Chi-restraints excluded: chain 0 residue 87 ASN Chi-restraints excluded: chain 0 residue 145 ASN Chi-restraints excluded: chain 0 residue 176 GLN Chi-restraints excluded: chain 0 residue 215 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 87 ASN Chi-restraints excluded: chain AA residue 176 GLN Chi-restraints excluded: chain AA residue 215 ILE Chi-restraints excluded: chain AB residue 52 ASP Chi-restraints excluded: chain AB residue 70 LEU Chi-restraints excluded: chain AB residue 87 ASN Chi-restraints excluded: chain AB residue 145 ASN Chi-restraints excluded: chain AB residue 176 GLN Chi-restraints excluded: chain AB residue 215 ILE Chi-restraints excluded: chain AC residue 52 ASP Chi-restraints excluded: chain AC residue 87 ASN Chi-restraints excluded: chain AC residue 146 VAL Chi-restraints excluded: chain AC residue 152 ASN Chi-restraints excluded: chain AC residue 153 GLN Chi-restraints excluded: chain AC residue 156 ASN Chi-restraints excluded: chain AC residue 176 GLN Chi-restraints excluded: chain AD residue 87 ASN Chi-restraints excluded: chain AD residue 176 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 211 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 225 ASN 6 118 ASN ** 6 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 225 ASN ** 0 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 118 ASN ** AA 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 173 ASN ** AB 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 118 ASN ** AC 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 209 ASN ** AD 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 113 GLN ** AD 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 157 ASN AD 209 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6723 r_free = 0.6723 target = 0.436099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.7971 r_free = 0.7971 target = 0.239815 restraints weight = 111985.218| |-----------------------------------------------------------------------------| r_work (start): 0.6280 rms_B_bonded: 11.22 r_work: 0.7364 rms_B_bonded: 6.63 restraints_weight: 2.0000 r_work (final): 0.7364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.9099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 17364 Z= 0.283 Angle : 0.944 9.666 23604 Z= 0.531 Chirality : 0.053 0.246 2772 Planarity : 0.004 0.047 3300 Dihedral : 10.778 39.579 2484 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 36.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 21.67 % Favored : 78.20 % Rotamer: Outliers : 5.35 % Allowed : 20.70 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.24 % 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 aren not related in a simple way. whole: -6.57 (0.09), residues: 2436 helix: -5.34 (0.11), residues: 84 sheet: -4.69 (0.18), residues: 372 loop : -4.72 (0.07), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYRAB 112 PHE 0.016 0.002 PHEAB 55 HIS 0.007 0.001 HISAC 182 Details of bonding type rmsd covalent geometry : bond 0.00542 (17364) covalent geometry : angle 0.94413 (23604) hydrogen bonds : bond 0.04004 ( 317) hydrogen bonds : angle 7.89031 ( 843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 230 time to evaluate : 0.874 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: 8 145 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7335 (m-40) REVERT: AC 52 ASP cc_start: 0.3775 (OUTLIER) cc_final: 0.2690 (p0) REVERT: AD 168 VAL cc_start: 0.3160 (t) cc_final: 0.2739 (m) outliers start: 97 outliers final: 86 residues processed: 314 average time/residue: 0.2213 time to fit residues: 112.8375 Evaluate side-chains 309 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 221 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 3 residue 52 ASP Chi-restraints excluded: chain 3 residue 73 SER Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 152 ASN Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 73 SER Chi-restraints excluded: chain 4 residue 88 GLN Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 145 ASN Chi-restraints excluded: chain 4 residue 152 ASN Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 217 VAL Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 73 SER Chi-restraints excluded: chain 5 residue 80 ASN Chi-restraints excluded: chain 5 residue 110 ASP Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 145 ASN Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 160 ILE Chi-restraints excluded: chain 5 residue 215 ILE Chi-restraints excluded: chain 6 residue 52 ASP Chi-restraints excluded: chain 6 residue 69 SER Chi-restraints excluded: chain 6 residue 73 SER Chi-restraints excluded: chain 6 residue 87 ASN Chi-restraints excluded: chain 6 residue 133 ASN Chi-restraints excluded: chain 6 residue 146 VAL Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 125 THR Chi-restraints excluded: chain 7 residue 131 LEU Chi-restraints excluded: chain 7 residue 146 VAL Chi-restraints excluded: chain 7 residue 152 ASN Chi-restraints excluded: chain 7 residue 215 ILE Chi-restraints excluded: chain 8 residue 52 ASP Chi-restraints excluded: chain 8 residue 69 SER Chi-restraints excluded: chain 8 residue 87 ASN Chi-restraints excluded: chain 8 residue 131 LEU Chi-restraints excluded: chain 8 residue 145 ASN Chi-restraints excluded: chain 8 residue 146 VAL Chi-restraints excluded: chain 8 residue 152 ASN Chi-restraints excluded: chain 8 residue 153 GLN Chi-restraints excluded: chain 8 residue 176 GLN Chi-restraints excluded: chain 9 residue 52 ASP Chi-restraints excluded: chain 9 residue 69 SER Chi-restraints excluded: chain 9 residue 73 SER Chi-restraints excluded: chain 9 residue 87 ASN Chi-restraints excluded: chain 9 residue 131 LEU Chi-restraints excluded: chain 9 residue 145 ASN Chi-restraints excluded: chain 9 residue 215 ILE Chi-restraints excluded: chain 9 residue 225 ASN Chi-restraints excluded: chain 9 residue 232 THR Chi-restraints excluded: chain 0 residue 69 SER Chi-restraints excluded: chain 0 residue 87 ASN Chi-restraints excluded: chain 0 residue 131 LEU Chi-restraints excluded: chain 0 residue 145 ASN Chi-restraints excluded: chain 0 residue 172 SER Chi-restraints excluded: chain 0 residue 176 GLN Chi-restraints excluded: chain 0 residue 215 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 69 SER Chi-restraints excluded: chain AA residue 77 LEU Chi-restraints excluded: chain AA residue 87 ASN Chi-restraints excluded: chain AA residue 146 VAL Chi-restraints excluded: chain AA residue 160 ILE Chi-restraints excluded: chain AA residue 176 GLN Chi-restraints excluded: chain AA residue 215 ILE Chi-restraints excluded: chain AB residue 52 ASP Chi-restraints excluded: chain AB residue 70 LEU Chi-restraints excluded: chain AB residue 87 ASN Chi-restraints excluded: chain AB residue 145 ASN Chi-restraints excluded: chain AB residue 176 GLN Chi-restraints excluded: chain AB residue 225 ASN Chi-restraints excluded: chain AC residue 52 ASP Chi-restraints excluded: chain AC residue 87 ASN Chi-restraints excluded: chain AC residue 133 ASN Chi-restraints excluded: chain AC residue 146 VAL Chi-restraints excluded: chain AC residue 152 ASN Chi-restraints excluded: chain AC residue 153 GLN Chi-restraints excluded: chain AC residue 176 GLN Chi-restraints excluded: chain AC residue 225 ASN Chi-restraints excluded: chain AD residue 87 ASN Chi-restraints excluded: chain AD residue 176 GLN Chi-restraints excluded: chain AD residue 225 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 116 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 163 optimal weight: 6.9990 chunk 234 optimal weight: 40.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 118 ASN 7 196 GLN ** 0 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 118 ASN ** AB 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 173 ASN ** AB 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 181 ASN ** AD 87 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 = 0.6632 r_free = 0.6632 target = 0.408021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.7707 r_free = 0.7707 target = 0.274738 restraints weight = 105893.602| |-----------------------------------------------------------------------------| r_work (start): 0.6369 rms_B_bonded: 11.20 r_work: 0.7516 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.7516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.9897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 17364 Z= 0.362 Angle : 1.029 11.024 23604 Z= 0.580 Chirality : 0.056 0.261 2772 Planarity : 0.005 0.046 3300 Dihedral : 11.195 42.676 2484 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 46.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 22.41 % Favored : 77.34 % Rotamer: Outliers : 5.96 % Allowed : 20.36 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.49 % 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 aren not related in a simple way. whole: -6.56 (0.09), residues: 2436 helix: -5.34 (0.11), residues: 84 sheet: -4.40 (0.18), residues: 444 loop : -4.74 (0.07), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYRAB 112 PHE 0.017 0.003 PHEAB 183 HIS 0.004 0.001 HISAC 182 Details of bonding type rmsd covalent geometry : bond 0.00683 (17364) covalent geometry : angle 1.02859 (23604) hydrogen bonds : bond 0.04855 ( 317) hydrogen bonds : angle 8.33372 ( 843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 221 time to evaluate : 0.896 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 218 ASN cc_start: 0.6501 (OUTLIER) cc_final: 0.6069 (p0) REVERT: 8 145 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7348 (m-40) REVERT: AC 52 ASP cc_start: 0.4073 (OUTLIER) cc_final: 0.2969 (p0) REVERT: AD 67 ASN cc_start: 0.5733 (t0) cc_final: 0.5024 (t0) outliers start: 108 outliers final: 99 residues processed: 312 average time/residue: 0.2642 time to fit residues: 133.1070 Evaluate side-chains 310 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 208 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 3 residue 52 ASP Chi-restraints excluded: chain 3 residue 73 SER Chi-restraints excluded: chain 3 residue 91 ASN Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 152 ASN Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 73 SER Chi-restraints excluded: chain 4 residue 88 GLN Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 145 ASN Chi-restraints excluded: chain 4 residue 146 VAL Chi-restraints excluded: chain 4 residue 152 ASN Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 217 VAL Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 73 SER Chi-restraints excluded: chain 5 residue 87 ASN Chi-restraints excluded: chain 5 residue 110 ASP Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 160 ILE Chi-restraints excluded: chain 5 residue 215 ILE Chi-restraints excluded: chain 5 residue 218 ASN Chi-restraints excluded: chain 5 residue 225 ASN Chi-restraints excluded: chain 6 residue 52 ASP Chi-restraints excluded: chain 6 residue 69 SER Chi-restraints excluded: chain 6 residue 73 SER Chi-restraints excluded: chain 6 residue 87 ASN Chi-restraints excluded: chain 6 residue 133 ASN Chi-restraints excluded: chain 6 residue 146 VAL Chi-restraints excluded: chain 7 residue 69 SER Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 87 ASN Chi-restraints excluded: chain 7 residue 125 THR Chi-restraints excluded: chain 7 residue 131 LEU Chi-restraints excluded: chain 7 residue 146 VAL Chi-restraints excluded: chain 7 residue 152 ASN Chi-restraints excluded: chain 8 residue 52 ASP Chi-restraints excluded: chain 8 residue 69 SER Chi-restraints excluded: chain 8 residue 73 SER Chi-restraints excluded: chain 8 residue 87 ASN Chi-restraints excluded: chain 8 residue 145 ASN Chi-restraints excluded: chain 8 residue 146 VAL Chi-restraints excluded: chain 8 residue 152 ASN Chi-restraints excluded: chain 8 residue 153 GLN Chi-restraints excluded: chain 8 residue 176 GLN Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 ASP Chi-restraints excluded: chain 9 residue 69 SER Chi-restraints excluded: chain 9 residue 87 ASN Chi-restraints excluded: chain 9 residue 131 LEU Chi-restraints excluded: chain 9 residue 145 ASN Chi-restraints excluded: chain 9 residue 152 ASN Chi-restraints excluded: chain 9 residue 172 SER Chi-restraints excluded: chain 9 residue 215 ILE Chi-restraints excluded: chain 9 residue 225 ASN Chi-restraints excluded: chain 9 residue 232 THR Chi-restraints excluded: chain 0 residue 69 SER Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 77 LEU Chi-restraints excluded: chain 0 residue 87 ASN Chi-restraints excluded: chain 0 residue 133 ASN Chi-restraints excluded: chain 0 residue 145 ASN Chi-restraints excluded: chain 0 residue 146 VAL Chi-restraints excluded: chain 0 residue 160 ILE Chi-restraints excluded: chain 0 residue 172 SER Chi-restraints excluded: chain 0 residue 176 GLN Chi-restraints excluded: chain 0 residue 215 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 69 SER Chi-restraints excluded: chain AA residue 87 ASN Chi-restraints excluded: chain AA residue 146 VAL Chi-restraints excluded: chain AA residue 160 ILE Chi-restraints excluded: chain AA residue 176 GLN Chi-restraints excluded: chain AA residue 215 ILE Chi-restraints excluded: chain AB residue 52 ASP Chi-restraints excluded: chain AB residue 70 LEU Chi-restraints excluded: chain AB residue 73 SER Chi-restraints excluded: chain AB residue 87 ASN Chi-restraints excluded: chain AB residue 133 ASN Chi-restraints excluded: chain AB residue 145 ASN Chi-restraints excluded: chain AB residue 160 ILE Chi-restraints excluded: chain AB residue 176 GLN Chi-restraints excluded: chain AB residue 215 ILE Chi-restraints excluded: chain AB residue 225 ASN Chi-restraints excluded: chain AB residue 231 LEU Chi-restraints excluded: chain AC residue 52 ASP Chi-restraints excluded: chain AC residue 87 ASN Chi-restraints excluded: chain AC residue 133 ASN Chi-restraints excluded: chain AC residue 146 VAL Chi-restraints excluded: chain AC residue 152 ASN Chi-restraints excluded: chain AC residue 153 GLN Chi-restraints excluded: chain AC residue 176 GLN Chi-restraints excluded: chain AC residue 206 ASN Chi-restraints excluded: chain AC residue 225 ASN Chi-restraints excluded: chain AD residue 80 ASN Chi-restraints excluded: chain AD residue 87 ASN Chi-restraints excluded: chain AD residue 176 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 56 optimal weight: 40.0000 chunk 3 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 209 ASN ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 209 ASN 6 209 ASN ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 225 ASN ** 0 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 173 ASN ** AB 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 181 ASN ** AD 87 ASN ** 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 = 0.6748 r_free = 0.6748 target = 0.435189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.7866 r_free = 0.7866 target = 0.238988 restraints weight = 112182.211| |-----------------------------------------------------------------------------| r_work (start): 0.6310 rms_B_bonded: 11.19 r_work: 0.7703 rms_B_bonded: 6.54 restraints_weight: 2.0000 r_work (final): 0.7703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.9748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17364 Z= 0.158 Angle : 0.859 9.092 23604 Z= 0.487 Chirality : 0.050 0.185 2772 Planarity : 0.003 0.044 3300 Dihedral : 10.036 37.938 2484 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 16.91 % Favored : 82.88 % Rotamer: Outliers : 3.59 % Allowed : 23.29 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.99 % 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 aren not related in a simple way. whole: -6.32 (0.09), residues: 2436 helix: -5.34 (0.11), residues: 84 sheet: -4.24 (0.26), residues: 252 loop : -4.64 (0.07), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYRAB 112 PHE 0.016 0.002 PHE 8 183 HIS 0.002 0.000 HISAC 182 Details of bonding type rmsd covalent geometry : bond 0.00314 (17364) covalent geometry : angle 0.85910 (23604) hydrogen bonds : bond 0.03048 ( 317) hydrogen bonds : angle 7.51567 ( 843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 0.924 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: 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: 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: 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: 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: 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: 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: 5 218 ASN cc_start: 0.6180 (p0) cc_final: 0.5636 (p0) REVERT: 0 133 ASN cc_start: 0.6493 (t0) cc_final: 0.4688 (t0) REVERT: 0 136 ASN cc_start: 0.6788 (t0) cc_final: 0.6473 (t0) REVERT: AA 133 ASN cc_start: 0.6630 (t0) cc_final: 0.5295 (t0) outliers start: 65 outliers final: 63 residues processed: 286 average time/residue: 0.2737 time to fit residues: 125.5510 Evaluate side-chains 284 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 3 residue 52 ASP Chi-restraints excluded: chain 3 residue 152 ASN Chi-restraints excluded: chain 3 residue 209 ASN Chi-restraints excluded: chain 4 residue 52 ASP Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 73 SER Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 145 ASN Chi-restraints excluded: chain 4 residue 152 ASN Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 5 residue 52 ASP Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 160 ILE Chi-restraints excluded: chain 5 residue 215 ILE Chi-restraints excluded: chain 6 residue 52 ASP Chi-restraints excluded: chain 6 residue 69 SER Chi-restraints excluded: chain 6 residue 73 SER Chi-restraints excluded: chain 6 residue 133 ASN Chi-restraints excluded: chain 6 residue 146 VAL Chi-restraints excluded: chain 7 residue 73 SER Chi-restraints excluded: chain 7 residue 125 THR Chi-restraints excluded: chain 7 residue 131 LEU Chi-restraints excluded: chain 7 residue 146 VAL Chi-restraints excluded: chain 7 residue 152 ASN Chi-restraints excluded: chain 8 residue 52 ASP Chi-restraints excluded: chain 8 residue 69 SER Chi-restraints excluded: chain 8 residue 131 LEU Chi-restraints excluded: chain 8 residue 146 VAL Chi-restraints excluded: chain 8 residue 152 ASN Chi-restraints excluded: chain 8 residue 176 GLN Chi-restraints excluded: chain 9 residue 52 ASP Chi-restraints excluded: chain 9 residue 69 SER Chi-restraints excluded: chain 9 residue 131 LEU Chi-restraints excluded: chain 9 residue 145 ASN Chi-restraints excluded: chain 9 residue 172 SER Chi-restraints excluded: chain 9 residue 215 ILE Chi-restraints excluded: chain 9 residue 232 THR Chi-restraints excluded: chain 0 residue 69 SER Chi-restraints excluded: chain 0 residue 77 LEU Chi-restraints excluded: chain 0 residue 87 ASN Chi-restraints excluded: chain 0 residue 176 GLN Chi-restraints excluded: chain 0 residue 215 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain AA residue 52 ASP Chi-restraints excluded: chain AA residue 69 SER Chi-restraints excluded: chain AA residue 87 ASN Chi-restraints excluded: chain AA residue 155 LYS Chi-restraints excluded: chain AA residue 176 GLN Chi-restraints excluded: chain AA residue 215 ILE Chi-restraints excluded: chain AB residue 52 ASP Chi-restraints excluded: chain AB residue 70 LEU Chi-restraints excluded: chain AB residue 87 ASN Chi-restraints excluded: chain AB residue 133 ASN Chi-restraints excluded: chain AB residue 145 ASN Chi-restraints excluded: chain AB residue 176 GLN Chi-restraints excluded: chain AB residue 215 ILE Chi-restraints excluded: chain AC residue 51 LYS Chi-restraints excluded: chain AC residue 87 ASN Chi-restraints excluded: chain AC residue 176 GLN Chi-restraints excluded: chain AC residue 206 ASN Chi-restraints excluded: chain AD residue 87 ASN Chi-restraints excluded: chain AD residue 176 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 209 ASN ** 5 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 173 ASN ** AB 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6907 r_free = 0.6907 target = 0.434865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.8330 r_free = 0.8330 target = 0.318217 restraints weight = 151663.944| |-----------------------------------------------------------------------------| r_work (start): 0.6408 rms_B_bonded: 10.50 r_work: 0.7816 rms_B_bonded: 5.89 restraints_weight: 2.0000 r_work (final): 0.7816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.9771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 17364 Z= 0.201 Angle : 0.990 59.182 23604 Z= 0.591 Chirality : 0.049 0.184 2772 Planarity : 0.003 0.044 3300 Dihedral : 10.022 37.820 2484 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 29.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 17.12 % Favored : 82.68 % Rotamer: Outliers : 3.70 % Allowed : 23.40 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.99 % 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 aren not related in a simple way. whole: -6.31 (0.09), residues: 2436 helix: -5.34 (0.11), residues: 84 sheet: -4.23 (0.26), residues: 252 loop : -4.64 (0.07), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYRAB 112 PHE 0.015 0.002 PHEAA 55 HIS 0.003 0.000 HISAC 182 Details of bonding type rmsd covalent geometry : bond 0.00388 (17364) covalent geometry : angle 0.98955 (23604) hydrogen bonds : bond 0.03082 ( 317) hydrogen bonds : angle 7.51348 ( 843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9416.09 seconds wall clock time: 160 minutes 44.69 seconds (9644.69 seconds total)