Starting phenix.real_space_refine on Thu Dec 26 06:50:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scc_25033/12_2024/7scc_25033_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scc_25033/12_2024/7scc_25033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7scc_25033/12_2024/7scc_25033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scc_25033/12_2024/7scc_25033.map" model { file = "/net/cci-nas-00/data/ceres_data/7scc_25033/12_2024/7scc_25033_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scc_25033/12_2024/7scc_25033_trim.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 222 5.16 5 C 27164 2.51 5 N 7240 2.21 5 O 8278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42904 Number of models: 1 Model: "" Number of chains: 62 Chain: "AA" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AB" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AC" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AD" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AE" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AF" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AH" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AI" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AJ" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AK" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AL" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AM" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AO" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "AQ" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 196} Chain: "AS" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2280 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 18, 'TRANS': 277} Chain breaks: 1 Chain: "AT" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1033 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "AU" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "AV" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "AW" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AX" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AY" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AZ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BA" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BB" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BD" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BE" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BF" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BG" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BH" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BI" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BK" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "BM" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 196} Chain: "BO" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1033 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "BP" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2280 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 18, 'TRANS': 277} Chain breaks: 1 Chain: "BQ" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "BR" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "AA" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AI" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AK" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AS" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'45D': 1} Classifications: {'undetermined': 1} Chain: "AW" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AY" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BB" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BF" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BG" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BI" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BP" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'45D': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.99, per 1000 atoms: 0.61 Number of scatterers: 42904 At special positions: 0 Unit cell: (162.75, 208.95, 127.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 222 16.00 O 8278 8.00 N 7240 7.00 C 27164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.54 Conformation dependent library (CDL) restraints added in 5.3 seconds 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10092 Finding SS restraints... Secondary structure from input PDB file: 268 helices and 6 sheets defined 75.3% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'AA' and resid 2 through 15 Processing helix chain 'AA' and resid 19 through 32 Processing helix chain 'AA' and resid 32 through 46 removed outlier: 3.691A pdb=" N ARGAA 36 " --> pdb=" O GLYAA 32 " (cutoff:3.500A) Processing helix chain 'AA' and resid 46 through 62 Processing helix chain 'AA' and resid 63 through 67 Processing helix chain 'AA' and resid 74 through 97 removed outlier: 3.878A pdb=" N CYSAA 81 " --> pdb=" O METAA 77 " (cutoff:3.500A) Processing helix chain 'AA' and resid 101 through 108 Processing helix chain 'AA' and resid 111 through 120 Processing helix chain 'AA' and resid 122 through 141 Processing helix chain 'AA' and resid 143 through 161 removed outlier: 4.033A pdb=" N ALAAA 147 " --> pdb=" O SERAA 143 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLUAA 148 " --> pdb=" O ASPAA 144 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYRAA 152 " --> pdb=" O GLUAA 148 " (cutoff:3.500A) Processing helix chain 'AB' and resid 3 through 15 removed outlier: 3.974A pdb=" N GLNAB 15 " --> pdb=" O SERAB 11 " (cutoff:3.500A) Processing helix chain 'AB' and resid 20 through 60 removed outlier: 4.089A pdb=" N GLUAB 35 " --> pdb=" O PHEAB 31 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEUAB 36 " --> pdb=" O ALAAB 32 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARGAB 39 " --> pdb=" O GLUAB 35 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASNAB 47 " --> pdb=" O VALAB 43 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALAAB 49 " --> pdb=" O SERAB 45 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THRAB 50 " --> pdb=" O ALAAB 46 " (cutoff:3.500A) Processing helix chain 'AB' and resid 74 through 99 Processing helix chain 'AB' and resid 101 through 108 Processing helix chain 'AB' and resid 111 through 120 Processing helix chain 'AB' and resid 122 through 142 Processing helix chain 'AB' and resid 142 through 161 removed outlier: 3.623A pdb=" N TYRAB 152 " --> pdb=" O GLUAB 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 3 through 15 Processing helix chain 'AC' and resid 19 through 46 removed outlier: 4.335A pdb=" N ARGAC 25 " --> pdb=" O GLYAC 21 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALAAC 34 " --> pdb=" O VALAC 30 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALAAC 35 " --> pdb=" O THRAC 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARGAC 36 " --> pdb=" O GLYAC 32 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SERAC 46 " --> pdb=" O THRAC 42 " (cutoff:3.500A) Processing helix chain 'AC' and resid 46 through 62 Processing helix chain 'AC' and resid 62 through 67 removed outlier: 4.402A pdb=" N VALAC 66 " --> pdb=" O ARGAC 62 " (cutoff:3.500A) Processing helix chain 'AC' and resid 76 through 99 Processing helix chain 'AC' and resid 101 through 109 removed outlier: 3.543A pdb=" N LEUAC 109 " --> pdb=" O GLUAC 105 " (cutoff:3.500A) Processing helix chain 'AC' and resid 111 through 118 Processing helix chain 'AC' and resid 122 through 141 Processing helix chain 'AC' and resid 143 through 161 removed outlier: 3.953A pdb=" N TYRAC 152 " --> pdb=" O GLUAC 148 " (cutoff:3.500A) Processing helix chain 'AD' and resid 3 through 15 removed outlier: 3.868A pdb=" N GLNAD 15 " --> pdb=" O SERAD 11 " (cutoff:3.500A) Processing helix chain 'AD' and resid 20 through 47 removed outlier: 4.116A pdb=" N GLUAD 35 " --> pdb=" O PHEAD 31 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEUAD 36 " --> pdb=" O ALAAD 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASNAD 47 " --> pdb=" O VALAD 43 " (cutoff:3.500A) Processing helix chain 'AD' and resid 47 through 58 Processing helix chain 'AD' and resid 74 through 99 Processing helix chain 'AD' and resid 102 through 108 Processing helix chain 'AD' and resid 111 through 120 Processing helix chain 'AD' and resid 122 through 142 Processing helix chain 'AD' and resid 143 through 161 removed outlier: 3.674A pdb=" N TYRAD 152 " --> pdb=" O GLUAD 148 " (cutoff:3.500A) Processing helix chain 'AE' and resid 3 through 15 Processing helix chain 'AE' and resid 19 through 46 removed outlier: 4.723A pdb=" N ALAAE 34 " --> pdb=" O VALAE 30 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALAAE 35 " --> pdb=" O THRAE 31 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SERAE 46 " --> pdb=" O THRAE 42 " (cutoff:3.500A) Processing helix chain 'AE' and resid 46 through 62 Processing helix chain 'AE' and resid 62 through 67 removed outlier: 4.230A pdb=" N VALAE 66 " --> pdb=" O ARGAE 62 " (cutoff:3.500A) Processing helix chain 'AE' and resid 74 through 99 Processing helix chain 'AE' and resid 101 through 109 Processing helix chain 'AE' and resid 111 through 120 Processing helix chain 'AE' and resid 122 through 140 Processing helix chain 'AE' and resid 142 through 161 removed outlier: 3.636A pdb=" N ALAAE 151 " --> pdb=" O ALAAE 147 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYRAE 152 " --> pdb=" O GLUAE 148 " (cutoff:3.500A) Processing helix chain 'AF' and resid 3 through 15 removed outlier: 4.252A pdb=" N GLNAF 15 " --> pdb=" O SERAF 11 " (cutoff:3.500A) Processing helix chain 'AF' and resid 20 through 60 removed outlier: 4.354A pdb=" N GLUAF 35 " --> pdb=" O PHEAF 31 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEUAF 36 " --> pdb=" O ALAAF 32 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALAAF 49 " --> pdb=" O SERAF 45 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N THRAF 50 " --> pdb=" O ALAAF 46 " (cutoff:3.500A) Processing helix chain 'AF' and resid 74 through 99 Processing helix chain 'AF' and resid 101 through 108 Processing helix chain 'AF' and resid 112 through 120 Processing helix chain 'AF' and resid 122 through 142 Processing helix chain 'AF' and resid 142 through 161 removed outlier: 4.080A pdb=" N GLUAF 148 " --> pdb=" O ASPAF 144 " (cutoff:3.500A) Processing helix chain 'AH' and resid 3 through 14 removed outlier: 3.681A pdb=" N GLUAH 14 " --> pdb=" O ASNAH 10 " (cutoff:3.500A) Processing helix chain 'AH' and resid 19 through 32 Processing helix chain 'AH' and resid 32 through 45 Processing helix chain 'AH' and resid 46 through 62 removed outlier: 3.603A pdb=" N GLNAH 60 " --> pdb=" O ASPAH 56 " (cutoff:3.500A) Processing helix chain 'AH' and resid 63 through 66 Processing helix chain 'AH' and resid 74 through 99 Processing helix chain 'AH' and resid 101 through 109 removed outlier: 3.985A pdb=" N LEUAH 109 " --> pdb=" O GLUAH 105 " (cutoff:3.500A) Processing helix chain 'AH' and resid 111 through 119 Processing helix chain 'AH' and resid 122 through 140 Processing helix chain 'AH' and resid 142 through 161 removed outlier: 3.819A pdb=" N TYRAH 152 " --> pdb=" O GLUAH 148 " (cutoff:3.500A) Processing helix chain 'AI' and resid 3 through 15 removed outlier: 3.938A pdb=" N GLNAI 15 " --> pdb=" O SERAI 11 " (cutoff:3.500A) Processing helix chain 'AI' and resid 20 through 47 removed outlier: 4.716A pdb=" N GLUAI 35 " --> pdb=" O PHEAI 31 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEUAI 36 " --> pdb=" O ALAAI 32 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARGAI 37 " --> pdb=" O SERAI 33 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASNAI 47 " --> pdb=" O VALAI 43 " (cutoff:3.500A) Processing helix chain 'AI' and resid 47 through 59 removed outlier: 4.094A pdb=" N VALAI 52 " --> pdb=" O ALAAI 48 " (cutoff:3.500A) Processing helix chain 'AI' and resid 73 through 99 removed outlier: 4.114A pdb=" N ARGAI 77 " --> pdb=" O TYRAI 73 " (cutoff:3.500A) Processing helix chain 'AI' and resid 101 through 108 Processing helix chain 'AI' and resid 111 through 120 Processing helix chain 'AI' and resid 122 through 142 removed outlier: 3.541A pdb=" N GLUAI 135 " --> pdb=" O GLNAI 131 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEUAI 140 " --> pdb=" O VALAI 136 " (cutoff:3.500A) Processing helix chain 'AI' and resid 143 through 161 Processing helix chain 'AJ' and resid 3 through 15 removed outlier: 3.515A pdb=" N GLUAJ 14 " --> pdb=" O ASNAJ 10 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 19 through 46 removed outlier: 5.090A pdb=" N ALAAJ 34 " --> pdb=" O VALAJ 30 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALAAJ 35 " --> pdb=" O THRAJ 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARGAJ 36 " --> pdb=" O GLYAJ 32 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 46 through 62 Processing helix chain 'AJ' and resid 63 through 66 Processing helix chain 'AJ' and resid 74 through 99 Processing helix chain 'AJ' and resid 101 through 109 removed outlier: 3.992A pdb=" N LEUAJ 109 " --> pdb=" O GLUAJ 105 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 111 through 119 Processing helix chain 'AJ' and resid 122 through 140 Processing helix chain 'AJ' and resid 142 through 161 removed outlier: 4.231A pdb=" N TYRAJ 152 " --> pdb=" O GLUAJ 148 " (cutoff:3.500A) Processing helix chain 'AK' and resid 3 through 15 removed outlier: 3.870A pdb=" N VALAK 8 " --> pdb=" O ALAAK 4 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILEAK 9 " --> pdb=" O ILEAK 5 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLNAK 15 " --> pdb=" O SERAK 11 " (cutoff:3.500A) Processing helix chain 'AK' and resid 20 through 47 removed outlier: 4.148A pdb=" N GLUAK 35 " --> pdb=" O PHEAK 31 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEUAK 36 " --> pdb=" O ALAAK 32 " (cutoff:3.500A) Processing helix chain 'AK' and resid 47 through 60 Processing helix chain 'AK' and resid 75 through 99 Processing helix chain 'AK' and resid 103 through 108 Processing helix chain 'AK' and resid 111 through 120 Processing helix chain 'AK' and resid 122 through 142 removed outlier: 3.694A pdb=" N GLYAK 142 " --> pdb=" O ALAAK 138 " (cutoff:3.500A) Processing helix chain 'AK' and resid 143 through 161 Processing helix chain 'AL' and resid 3 through 15 Processing helix chain 'AL' and resid 19 through 46 removed outlier: 4.373A pdb=" N ALAAL 34 " --> pdb=" O VALAL 30 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALAAL 35 " --> pdb=" O THRAL 31 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SERAL 46 " --> pdb=" O THRAL 42 " (cutoff:3.500A) Processing helix chain 'AL' and resid 46 through 62 Processing helix chain 'AL' and resid 62 through 67 removed outlier: 4.376A pdb=" N VALAL 66 " --> pdb=" O ARGAL 62 " (cutoff:3.500A) Processing helix chain 'AL' and resid 74 through 99 Processing helix chain 'AL' and resid 101 through 109 Processing helix chain 'AL' and resid 111 through 120 Processing helix chain 'AL' and resid 122 through 140 Processing helix chain 'AL' and resid 142 through 161 removed outlier: 4.033A pdb=" N TYRAL 152 " --> pdb=" O GLUAL 148 " (cutoff:3.500A) Processing helix chain 'AM' and resid 3 through 15 removed outlier: 3.576A pdb=" N GLNAM 15 " --> pdb=" O SERAM 11 " (cutoff:3.500A) Processing helix chain 'AM' and resid 20 through 58 removed outlier: 4.330A pdb=" N GLUAM 35 " --> pdb=" O PHEAM 31 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEUAM 36 " --> pdb=" O ALAAM 32 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALAAM 49 " --> pdb=" O SERAM 45 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N THRAM 50 " --> pdb=" O ALAAM 46 " (cutoff:3.500A) Processing helix chain 'AM' and resid 73 through 99 removed outlier: 3.884A pdb=" N ARGAM 77 " --> pdb=" O TYRAM 73 " (cutoff:3.500A) Processing helix chain 'AM' and resid 101 through 108 removed outlier: 3.543A pdb=" N GLUAM 106 " --> pdb=" O SERAM 102 " (cutoff:3.500A) Processing helix chain 'AM' and resid 111 through 120 Processing helix chain 'AM' and resid 122 through 142 Processing helix chain 'AM' and resid 143 through 161 removed outlier: 3.771A pdb=" N TYRAM 152 " --> pdb=" O GLUAM 148 " (cutoff:3.500A) Processing helix chain 'AO' and resid 21 through 25 Processing helix chain 'AO' and resid 32 through 46 removed outlier: 4.258A pdb=" N PHEAO 37 " --> pdb=" O TYRAO 33 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARGAO 38 " --> pdb=" O ASPAO 34 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 689 through 696 Processing helix chain 'AQ' and resid 702 through 711 removed outlier: 3.749A pdb=" N ASNAQ 711 " --> pdb=" O ALAAQ 707 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 715 through 719 Processing helix chain 'AQ' and resid 731 through 748 Processing helix chain 'AQ' and resid 760 through 769 Processing helix chain 'AQ' and resid 773 through 783 Processing helix chain 'AQ' and resid 784 through 791 Processing helix chain 'AQ' and resid 796 through 808 Processing helix chain 'AQ' and resid 815 through 829 Processing helix chain 'AQ' and resid 829 through 841 removed outlier: 4.280A pdb=" N ALAAQ 833 " --> pdb=" O GLNAQ 829 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHEAQ 834 " --> pdb=" O GLYAQ 830 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 841 through 849 Processing helix chain 'AQ' and resid 864 through 874 Processing helix chain 'AS' and resid 19 through 31 removed outlier: 3.579A pdb=" N GLNAS 30 " --> pdb=" O ALAAS 26 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEUAS 31 " --> pdb=" O ARGAS 27 " (cutoff:3.500A) Processing helix chain 'AS' and resid 32 through 47 Processing helix chain 'AS' and resid 55 through 59 Processing helix chain 'AS' and resid 60 through 63 removed outlier: 3.620A pdb=" N LEUAS 63 " --> pdb=" O SERAS 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'AS' and resid 60 through 63' Processing helix chain 'AS' and resid 64 through 74 Processing helix chain 'AS' and resid 75 through 88 Processing helix chain 'AS' and resid 92 through 100 Processing helix chain 'AS' and resid 102 through 120 Processing helix chain 'AS' and resid 132 through 145 Processing helix chain 'AS' and resid 146 through 160 removed outlier: 4.194A pdb=" N ASPAS 160 " --> pdb=" O ASNAS 156 " (cutoff:3.500A) Processing helix chain 'AS' and resid 195 through 207 removed outlier: 3.745A pdb=" N ASNAS 206 " --> pdb=" O METAS 202 " (cutoff:3.500A) Processing helix chain 'AS' and resid 209 through 215 removed outlier: 3.729A pdb=" N GLUAS 215 " --> pdb=" O ASPAS 211 " (cutoff:3.500A) Processing helix chain 'AS' and resid 233 through 244 Processing helix chain 'AS' and resid 261 through 263 No H-bonds generated for 'chain 'AS' and resid 261 through 263' Processing helix chain 'AT' and resid 195 through 208 Processing helix chain 'AT' and resid 209 through 214 Processing helix chain 'AT' and resid 233 through 244 Processing helix chain 'AT' and resid 261 through 263 No H-bonds generated for 'chain 'AT' and resid 261 through 263' Processing helix chain 'AU' and resid 215 through 226 removed outlier: 4.054A pdb=" N GLYAU 220 " --> pdb=" O METAU 216 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N METAU 221 " --> pdb=" O ASNAU 217 " (cutoff:3.500A) Processing helix chain 'AV' and resid 215 through 226 removed outlier: 4.336A pdb=" N GLYAV 220 " --> pdb=" O METAV 216 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N METAV 221 " --> pdb=" O ASNAV 217 " (cutoff:3.500A) Processing helix chain 'AW' and resid 3 through 14 Processing helix chain 'AW' and resid 19 through 46 removed outlier: 5.019A pdb=" N ALAAW 34 " --> pdb=" O VALAW 30 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALAAW 35 " --> pdb=" O THRAW 31 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SERAW 46 " --> pdb=" O THRAW 42 " (cutoff:3.500A) Processing helix chain 'AW' and resid 46 through 62 Processing helix chain 'AW' and resid 62 through 67 removed outlier: 4.230A pdb=" N VALAW 66 " --> pdb=" O ARGAW 62 " (cutoff:3.500A) Processing helix chain 'AW' and resid 74 through 99 Processing helix chain 'AW' and resid 101 through 109 Processing helix chain 'AW' and resid 111 through 120 Processing helix chain 'AW' and resid 122 through 140 Processing helix chain 'AW' and resid 142 through 161 removed outlier: 3.686A pdb=" N ALAAW 147 " --> pdb=" O SERAW 143 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLUAW 148 " --> pdb=" O ASPAW 144 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYRAW 152 " --> pdb=" O GLUAW 148 " (cutoff:3.500A) Processing helix chain 'AX' and resid 5 through 15 removed outlier: 3.913A pdb=" N GLNAX 15 " --> pdb=" O SERAX 11 " (cutoff:3.500A) Processing helix chain 'AX' and resid 20 through 47 removed outlier: 4.331A pdb=" N GLUAX 35 " --> pdb=" O PHEAX 31 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEUAX 36 " --> pdb=" O ALAAX 32 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASNAX 47 " --> pdb=" O VALAX 43 " (cutoff:3.500A) Processing helix chain 'AX' and resid 47 through 60 removed outlier: 4.134A pdb=" N VALAX 52 " --> pdb=" O ALAAX 48 " (cutoff:3.500A) Processing helix chain 'AX' and resid 74 through 99 Processing helix chain 'AX' and resid 101 through 108 removed outlier: 3.581A pdb=" N VALAX 108 " --> pdb=" O LEUAX 104 " (cutoff:3.500A) Processing helix chain 'AX' and resid 111 through 120 Processing helix chain 'AX' and resid 122 through 142 Processing helix chain 'AX' and resid 142 through 161 removed outlier: 3.863A pdb=" N TYRAX 152 " --> pdb=" O GLUAX 148 " (cutoff:3.500A) Processing helix chain 'AY' and resid 3 through 14 removed outlier: 3.694A pdb=" N GLUAY 14 " --> pdb=" O ASNAY 10 " (cutoff:3.500A) Processing helix chain 'AY' and resid 19 through 46 removed outlier: 4.502A pdb=" N ARGAY 25 " --> pdb=" O GLYAY 21 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALAAY 34 " --> pdb=" O VALAY 30 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALAAY 35 " --> pdb=" O THRAY 31 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGAY 36 " --> pdb=" O GLYAY 32 " (cutoff:3.500A) Processing helix chain 'AY' and resid 46 through 62 Processing helix chain 'AY' and resid 76 through 99 Processing helix chain 'AY' and resid 101 through 109 removed outlier: 3.720A pdb=" N LEUAY 109 " --> pdb=" O GLUAY 105 " (cutoff:3.500A) Processing helix chain 'AY' and resid 111 through 118 Processing helix chain 'AY' and resid 122 through 141 Processing helix chain 'AY' and resid 143 through 161 removed outlier: 3.623A pdb=" N ALAAY 151 " --> pdb=" O ALAAY 147 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYRAY 152 " --> pdb=" O GLUAY 148 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 3 through 14 Processing helix chain 'AZ' and resid 20 through 47 removed outlier: 4.134A pdb=" N GLUAZ 35 " --> pdb=" O PHEAZ 31 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEUAZ 36 " --> pdb=" O ALAAZ 32 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 47 through 60 Processing helix chain 'AZ' and resid 74 through 99 Processing helix chain 'AZ' and resid 102 through 108 Processing helix chain 'AZ' and resid 111 through 120 Processing helix chain 'AZ' and resid 122 through 142 Processing helix chain 'AZ' and resid 143 through 161 removed outlier: 3.589A pdb=" N TYRAZ 152 " --> pdb=" O GLUAZ 148 " (cutoff:3.500A) Processing helix chain 'BA' and resid 3 through 15 Processing helix chain 'BA' and resid 19 through 46 removed outlier: 4.601A pdb=" N ALABA 34 " --> pdb=" O VALBA 30 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALABA 35 " --> pdb=" O THRBA 31 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SERBA 46 " --> pdb=" O THRBA 42 " (cutoff:3.500A) Processing helix chain 'BA' and resid 46 through 62 Processing helix chain 'BA' and resid 62 through 67 removed outlier: 4.157A pdb=" N VALBA 66 " --> pdb=" O ARGBA 62 " (cutoff:3.500A) Processing helix chain 'BA' and resid 74 through 99 Processing helix chain 'BA' and resid 101 through 109 removed outlier: 3.547A pdb=" N LEUBA 109 " --> pdb=" O GLUBA 105 " (cutoff:3.500A) Processing helix chain 'BA' and resid 111 through 120 Processing helix chain 'BA' and resid 122 through 140 removed outlier: 3.563A pdb=" N LEUBA 140 " --> pdb=" O VALBA 136 " (cutoff:3.500A) Processing helix chain 'BA' and resid 142 through 161 removed outlier: 3.612A pdb=" N ALABA 151 " --> pdb=" O ALABA 147 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYRBA 152 " --> pdb=" O GLUBA 148 " (cutoff:3.500A) Processing helix chain 'BB' and resid 3 through 15 removed outlier: 4.017A pdb=" N GLNBB 15 " --> pdb=" O SERBB 11 " (cutoff:3.500A) Processing helix chain 'BB' and resid 20 through 47 removed outlier: 4.369A pdb=" N GLUBB 35 " --> pdb=" O PHEBB 31 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEUBB 36 " --> pdb=" O ALABB 32 " (cutoff:3.500A) Processing helix chain 'BB' and resid 47 through 60 Processing helix chain 'BB' and resid 74 through 99 Processing helix chain 'BB' and resid 101 through 108 Processing helix chain 'BB' and resid 111 through 120 Processing helix chain 'BB' and resid 122 through 161 removed outlier: 7.181A pdb=" N ALABB 143 " --> pdb=" O SERBB 139 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ASPBB 144 " --> pdb=" O LEUBB 140 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALABB 145 " --> pdb=" O VALBB 141 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLUBB 148 " --> pdb=" O ASPBB 144 " (cutoff:3.500A) Processing helix chain 'BD' and resid 3 through 14 Processing helix chain 'BD' and resid 19 through 46 removed outlier: 5.288A pdb=" N ALABD 34 " --> pdb=" O VALBD 30 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALABD 35 " --> pdb=" O THRBD 31 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARGBD 36 " --> pdb=" O GLYBD 32 " (cutoff:3.500A) Processing helix chain 'BD' and resid 46 through 62 Processing helix chain 'BD' and resid 63 through 66 Processing helix chain 'BD' and resid 74 through 99 removed outlier: 3.572A pdb=" N ALABD 79 " --> pdb=" O GLUBD 75 " (cutoff:3.500A) Processing helix chain 'BD' and resid 101 through 109 removed outlier: 3.582A pdb=" N LEUBD 109 " --> pdb=" O GLUBD 105 " (cutoff:3.500A) Processing helix chain 'BD' and resid 111 through 120 Processing helix chain 'BD' and resid 122 through 141 removed outlier: 3.613A pdb=" N VALBD 126 " --> pdb=" O PROBD 122 " (cutoff:3.500A) Processing helix chain 'BD' and resid 142 through 161 removed outlier: 3.658A pdb=" N GLUBD 148 " --> pdb=" O ASPBD 144 " (cutoff:3.500A) Processing helix chain 'BE' and resid 3 through 15 removed outlier: 3.683A pdb=" N GLNBE 15 " --> pdb=" O SERBE 11 " (cutoff:3.500A) Processing helix chain 'BE' and resid 20 through 47 removed outlier: 4.260A pdb=" N LYSBE 26 " --> pdb=" O ALABE 22 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLUBE 35 " --> pdb=" O PHEBE 31 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEUBE 36 " --> pdb=" O ALABE 32 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARGBE 37 " --> pdb=" O SERBE 33 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASNBE 47 " --> pdb=" O VALBE 43 " (cutoff:3.500A) Processing helix chain 'BE' and resid 47 through 59 removed outlier: 3.563A pdb=" N ILEBE 51 " --> pdb=" O ASNBE 47 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VALBE 52 " --> pdb=" O ALABE 48 " (cutoff:3.500A) Processing helix chain 'BE' and resid 74 through 99 Processing helix chain 'BE' and resid 101 through 108 Processing helix chain 'BE' and resid 111 through 120 Processing helix chain 'BE' and resid 122 through 142 Processing helix chain 'BE' and resid 143 through 161 Processing helix chain 'BF' and resid 3 through 15 Processing helix chain 'BF' and resid 19 through 46 removed outlier: 5.136A pdb=" N ALABF 34 " --> pdb=" O VALBF 30 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALABF 35 " --> pdb=" O THRBF 31 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARGBF 36 " --> pdb=" O GLYBF 32 " (cutoff:3.500A) Processing helix chain 'BF' and resid 46 through 62 Processing helix chain 'BF' and resid 62 through 67 removed outlier: 4.338A pdb=" N VALBF 66 " --> pdb=" O ARGBF 62 " (cutoff:3.500A) Processing helix chain 'BF' and resid 74 through 99 Processing helix chain 'BF' and resid 101 through 109 Processing helix chain 'BF' and resid 111 through 120 Processing helix chain 'BF' and resid 122 through 140 Processing helix chain 'BF' and resid 142 through 161 removed outlier: 4.031A pdb=" N TYRBF 152 " --> pdb=" O GLUBF 148 " (cutoff:3.500A) Processing helix chain 'BG' and resid 3 through 15 removed outlier: 4.346A pdb=" N GLNBG 15 " --> pdb=" O SERBG 11 " (cutoff:3.500A) Processing helix chain 'BG' and resid 20 through 47 removed outlier: 4.096A pdb=" N GLUBG 35 " --> pdb=" O PHEBG 31 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEUBG 36 " --> pdb=" O ALABG 32 " (cutoff:3.500A) Processing helix chain 'BG' and resid 47 through 58 removed outlier: 3.764A pdb=" N VALBG 52 " --> pdb=" O ALABG 48 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYSBG 53 " --> pdb=" O ALABG 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLUBG 54 " --> pdb=" O THRBG 50 " (cutoff:3.500A) Processing helix chain 'BG' and resid 75 through 99 Processing helix chain 'BG' and resid 102 through 108 Processing helix chain 'BG' and resid 111 through 120 Processing helix chain 'BG' and resid 122 through 142 Processing helix chain 'BG' and resid 142 through 161 removed outlier: 4.019A pdb=" N GLUBG 148 " --> pdb=" O ASPBG 144 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N METBG 149 " --> pdb=" O ALABG 145 " (cutoff:3.500A) Processing helix chain 'BH' and resid 3 through 15 Processing helix chain 'BH' and resid 19 through 46 removed outlier: 4.418A pdb=" N ALABH 34 " --> pdb=" O VALBH 30 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALABH 35 " --> pdb=" O THRBH 31 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SERBH 46 " --> pdb=" O THRBH 42 " (cutoff:3.500A) Processing helix chain 'BH' and resid 46 through 62 Processing helix chain 'BH' and resid 62 through 67 removed outlier: 4.381A pdb=" N VALBH 66 " --> pdb=" O ARGBH 62 " (cutoff:3.500A) Processing helix chain 'BH' and resid 74 through 99 Processing helix chain 'BH' and resid 101 through 109 Processing helix chain 'BH' and resid 111 through 120 Processing helix chain 'BH' and resid 122 through 139 Processing helix chain 'BH' and resid 142 through 161 removed outlier: 3.986A pdb=" N TYRBH 152 " --> pdb=" O GLUBH 148 " (cutoff:3.500A) Processing helix chain 'BI' and resid 3 through 16 removed outlier: 3.596A pdb=" N GLNBI 15 " --> pdb=" O SERBI 11 " (cutoff:3.500A) Processing helix chain 'BI' and resid 20 through 47 removed outlier: 4.220A pdb=" N GLUBI 35 " --> pdb=" O PHEBI 31 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEUBI 36 " --> pdb=" O ALABI 32 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASNBI 47 " --> pdb=" O VALBI 43 " (cutoff:3.500A) Processing helix chain 'BI' and resid 47 through 58 removed outlier: 3.935A pdb=" N VALBI 52 " --> pdb=" O ALABI 48 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYSBI 53 " --> pdb=" O ALABI 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLUBI 54 " --> pdb=" O THRBI 50 " (cutoff:3.500A) Processing helix chain 'BI' and resid 74 through 99 Processing helix chain 'BI' and resid 101 through 108 removed outlier: 3.665A pdb=" N GLUBI 106 " --> pdb=" O SERBI 102 " (cutoff:3.500A) Processing helix chain 'BI' and resid 111 through 120 Processing helix chain 'BI' and resid 122 through 142 removed outlier: 3.534A pdb=" N LEUBI 140 " --> pdb=" O VALBI 136 " (cutoff:3.500A) Processing helix chain 'BI' and resid 143 through 161 removed outlier: 3.537A pdb=" N TYRBI 152 " --> pdb=" O GLUBI 148 " (cutoff:3.500A) Processing helix chain 'BK' and resid 32 through 46 removed outlier: 4.275A pdb=" N PHEBK 37 " --> pdb=" O TYRBK 33 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARGBK 38 " --> pdb=" O ASPBK 34 " (cutoff:3.500A) Processing helix chain 'BM' and resid 689 through 696 Processing helix chain 'BM' and resid 702 through 711 removed outlier: 4.158A pdb=" N ASNBM 711 " --> pdb=" O ALABM 707 " (cutoff:3.500A) Processing helix chain 'BM' and resid 715 through 719 Processing helix chain 'BM' and resid 731 through 747 Processing helix chain 'BM' and resid 760 through 769 Processing helix chain 'BM' and resid 773 through 783 Processing helix chain 'BM' and resid 784 through 792 Processing helix chain 'BM' and resid 796 through 808 Processing helix chain 'BM' and resid 815 through 830 Processing helix chain 'BM' and resid 831 through 840 Processing helix chain 'BM' and resid 841 through 848 Processing helix chain 'BM' and resid 864 through 874 Processing helix chain 'BO' and resid 195 through 208 removed outlier: 3.575A pdb=" N LEUBO 199 " --> pdb=" O ASNBO 195 " (cutoff:3.500A) Processing helix chain 'BO' and resid 209 through 214 Processing helix chain 'BO' and resid 233 through 244 Processing helix chain 'BO' and resid 261 through 263 No H-bonds generated for 'chain 'BO' and resid 261 through 263' Processing helix chain 'BP' and resid 19 through 31 removed outlier: 3.645A pdb=" N GLNBP 30 " --> pdb=" O ALABP 26 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEUBP 31 " --> pdb=" O ARGBP 27 " (cutoff:3.500A) Processing helix chain 'BP' and resid 32 through 46 Processing helix chain 'BP' and resid 55 through 59 Processing helix chain 'BP' and resid 60 through 63 removed outlier: 3.521A pdb=" N LEUBP 63 " --> pdb=" O SERBP 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 60 through 63' Processing helix chain 'BP' and resid 64 through 74 Processing helix chain 'BP' and resid 75 through 89 Processing helix chain 'BP' and resid 92 through 100 Processing helix chain 'BP' and resid 102 through 119 Processing helix chain 'BP' and resid 132 through 145 Processing helix chain 'BP' and resid 146 through 160 removed outlier: 4.201A pdb=" N ASPBP 160 " --> pdb=" O ASNBP 156 " (cutoff:3.500A) Processing helix chain 'BP' and resid 195 through 207 removed outlier: 3.568A pdb=" N ASNBP 206 " --> pdb=" O METBP 202 " (cutoff:3.500A) Processing helix chain 'BP' and resid 209 through 217 removed outlier: 3.708A pdb=" N GLUBP 215 " --> pdb=" O ASPBP 211 " (cutoff:3.500A) Processing helix chain 'BP' and resid 233 through 244 Processing helix chain 'BP' and resid 261 through 263 No H-bonds generated for 'chain 'BP' and resid 261 through 263' Processing helix chain 'BQ' and resid 215 through 226 removed outlier: 4.017A pdb=" N GLYBQ 220 " --> pdb=" O METBQ 216 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N METBQ 221 " --> pdb=" O ASNBQ 217 " (cutoff:3.500A) Processing helix chain 'BR' and resid 215 through 226 removed outlier: 4.174A pdb=" N GLYBR 220 " --> pdb=" O METBR 216 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N METBR 221 " --> pdb=" O ASNBR 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AO' and resid 26 through 31 removed outlier: 6.782A pdb=" N CYSAO 9 " --> pdb=" O ILEAO 50 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILEAO 50 " --> pdb=" O CYSAO 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AS' and resid 231 through 232 removed outlier: 6.579A pdb=" N ALAAS 222 " --> pdb=" O VALAS 301 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILEAS 303 " --> pdb=" O ALAAS 222 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLNAS 224 " --> pdb=" O ILEAS 303 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEUAS 305 " --> pdb=" O GLNAS 224 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLNAS 266 " --> pdb=" O THRAS 257 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THRAS 257 " --> pdb=" O GLNAS 266 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYSAS 268 " --> pdb=" O GLYAS 255 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLYAS 255 " --> pdb=" O LYSAS 268 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THRAS 270 " --> pdb=" O GLUAS 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AT' and resid 231 through 232 removed outlier: 6.523A pdb=" N PHEAT 299 " --> pdb=" O THRAT 218 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASPAT 220 " --> pdb=" O PHEAT 299 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VALAT 301 " --> pdb=" O ASPAT 220 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALAAT 222 " --> pdb=" O VALAT 301 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILEAT 303 " --> pdb=" O ALAAT 222 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLNAT 224 " --> pdb=" O ILEAT 303 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEUAT 305 " --> pdb=" O GLNAT 224 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N METAT 284 " --> pdb=" O VALAT 273 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLNAT 266 " --> pdb=" O THRAT 257 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THRAT 257 " --> pdb=" O GLNAT 266 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYSAT 268 " --> pdb=" O GLYAT 255 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLYAT 255 " --> pdb=" O LYSAT 268 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THRAT 270 " --> pdb=" O GLUAT 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'BK' and resid 26 through 31 removed outlier: 6.864A pdb=" N CYSBK 9 " --> pdb=" O ILEBK 50 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILEBK 50 " --> pdb=" O CYSBK 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'BO' and resid 231 through 232 removed outlier: 6.380A pdb=" N PHEBO 299 " --> pdb=" O THRBO 218 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASPBO 220 " --> pdb=" O PHEBO 299 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N VALBO 301 " --> pdb=" O ASPBO 220 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALABO 222 " --> pdb=" O VALBO 301 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILEBO 303 " --> pdb=" O ALABO 222 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLNBO 224 " --> pdb=" O ILEBO 303 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEUBO 305 " --> pdb=" O GLNBO 224 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N METBO 284 " --> pdb=" O VALBO 273 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYSBO 272 " --> pdb=" O PROBO 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'BP' and resid 231 through 232 removed outlier: 6.656A pdb=" N ALABP 222 " --> pdb=" O VALBP 301 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILEBP 303 " --> pdb=" O ALABP 222 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLNBP 224 " --> pdb=" O ILEBP 303 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEUBP 305 " --> pdb=" O GLNBP 224 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLNBP 266 " --> pdb=" O THRBP 257 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THRBP 257 " --> pdb=" O GLNBP 266 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYSBP 268 " --> pdb=" O GLYBP 255 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLYBP 255 " --> pdb=" O LYSBP 268 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THRBP 270 " --> pdb=" O GLUBP 253 " (cutoff:3.500A) 2981 hydrogen bonds defined for protein. 8868 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: 16.87 Time building geometry restraints manager: 14.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10016 1.33 - 1.45: 8665 1.45 - 1.57: 24505 1.57 - 1.69: 0 1.69 - 1.81: 398 Bond restraints: 43584 Sorted by residual: bond pdb=" C34 45DAS 400 " pdb=" C36 45DAS 400 " ideal model delta sigma weight residual 1.444 1.534 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C34 45DBP 400 " pdb=" C36 45DBP 400 " ideal model delta sigma weight residual 1.444 1.532 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CGA CYCBD 200 " pdb=" O2A CYCBD 200 " ideal model delta sigma weight residual 1.249 1.309 -0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" CGD CYCAA 200 " pdb=" O2D CYCAA 200 " ideal model delta sigma weight residual 1.249 1.308 -0.059 2.00e-02 2.50e+03 8.71e+00 bond pdb=" CGD CYCAF 200 " pdb=" O2D CYCAF 200 " ideal model delta sigma weight residual 1.249 1.308 -0.059 2.00e-02 2.50e+03 8.69e+00 ... (remaining 43579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 58582 3.05 - 6.10: 454 6.10 - 9.16: 41 9.16 - 12.21: 7 12.21 - 15.26: 6 Bond angle restraints: 59090 Sorted by residual: angle pdb=" C1B CYCAF 200 " pdb=" CHB CYCAF 200 " pdb=" C4A CYCAF 200 " ideal model delta sigma weight residual 126.10 141.36 -15.26 3.00e+00 1.11e-01 2.59e+01 angle pdb=" C1B CYCBD 200 " pdb=" CHB CYCBD 200 " pdb=" C4A CYCBD 200 " ideal model delta sigma weight residual 126.10 140.84 -14.74 3.00e+00 1.11e-01 2.41e+01 angle pdb=" C1B CYCBH 200 " pdb=" CHB CYCBH 200 " pdb=" C4A CYCBH 200 " ideal model delta sigma weight residual 126.10 140.65 -14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C1B CYCBA 200 " pdb=" CHB CYCBA 200 " pdb=" C4A CYCBA 200 " ideal model delta sigma weight residual 126.10 140.37 -14.27 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C1B CYCBB 200 " pdb=" CHB CYCBB 200 " pdb=" C4A CYCBB 200 " ideal model delta sigma weight residual 126.10 140.21 -14.11 3.00e+00 1.11e-01 2.21e+01 ... (remaining 59085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 25253 21.47 - 42.94: 1453 42.94 - 64.41: 156 64.41 - 85.88: 57 85.88 - 107.35: 9 Dihedral angle restraints: 26928 sinusoidal: 11134 harmonic: 15794 Sorted by residual: dihedral pdb=" CA SERBE 33 " pdb=" C SERBE 33 " pdb=" N GLYBE 34 " pdb=" CA GLYBE 34 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ILEBQ 242 " pdb=" C ILEBQ 242 " pdb=" N GLUBQ 243 " pdb=" CA GLUBQ 243 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SERAI 33 " pdb=" C SERAI 33 " pdb=" N GLYAI 34 " pdb=" CA GLYAI 34 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 26925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 5233 0.045 - 0.090: 1182 0.090 - 0.136: 217 0.136 - 0.181: 29 0.181 - 0.226: 7 Chirality restraints: 6668 Sorted by residual: chirality pdb=" C3C CYCBD 200 " pdb=" C2C CYCBD 200 " pdb=" C4C CYCBD 200 " pdb=" CAC CYCBD 200 " both_signs ideal model delta sigma weight residual False 2.62 2.84 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3C CYCAW 200 " pdb=" C2C CYCAW 200 " pdb=" C4C CYCAW 200 " pdb=" CAC CYCAW 200 " both_signs ideal model delta sigma weight residual False 2.62 2.84 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILEBQ 242 " pdb=" CA ILEBQ 242 " pdb=" CG1 ILEBQ 242 " pdb=" CG2 ILEBQ 242 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 6665 not shown) Planarity restraints: 7602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CYCAC 200 " -0.032 2.00e-02 2.50e+03 1.48e-01 4.95e+02 pdb=" OB CYCAC 200 " 0.092 2.00e-02 2.50e+03 pdb=" C1B CYCAC 200 " -0.016 2.00e-02 2.50e+03 pdb=" C2B CYCAC 200 " 0.098 2.00e-02 2.50e+03 pdb=" C3B CYCAC 200 " 0.133 2.00e-02 2.50e+03 pdb=" C4B CYCAC 200 " 0.060 2.00e-02 2.50e+03 pdb=" CAB CYCAC 200 " -0.314 2.00e-02 2.50e+03 pdb=" CHB CYCAC 200 " -0.181 2.00e-02 2.50e+03 pdb=" CMB CYCAC 200 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAY 200 " 0.033 2.00e-02 2.50e+03 1.38e-01 4.30e+02 pdb=" OB CYCAY 200 " -0.078 2.00e-02 2.50e+03 pdb=" C1B CYCAY 200 " 0.007 2.00e-02 2.50e+03 pdb=" C2B CYCAY 200 " -0.101 2.00e-02 2.50e+03 pdb=" C3B CYCAY 200 " -0.134 2.00e-02 2.50e+03 pdb=" C4B CYCAY 200 " -0.055 2.00e-02 2.50e+03 pdb=" CAB CYCAY 200 " 0.292 2.00e-02 2.50e+03 pdb=" CHB CYCAY 200 " 0.172 2.00e-02 2.50e+03 pdb=" CMB CYCAY 200 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCBF 200 " -0.016 2.00e-02 2.50e+03 1.25e-01 3.54e+02 pdb=" OB CYCBF 200 " 0.061 2.00e-02 2.50e+03 pdb=" C1B CYCBF 200 " -0.022 2.00e-02 2.50e+03 pdb=" C2B CYCBF 200 " 0.079 2.00e-02 2.50e+03 pdb=" C3B CYCBF 200 " 0.123 2.00e-02 2.50e+03 pdb=" C4B CYCBF 200 " 0.061 2.00e-02 2.50e+03 pdb=" CAB CYCBF 200 " -0.266 2.00e-02 2.50e+03 pdb=" CHB CYCBF 200 " -0.154 2.00e-02 2.50e+03 pdb=" CMB CYCBF 200 " 0.133 2.00e-02 2.50e+03 ... (remaining 7599 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 726 2.62 - 3.19: 43842 3.19 - 3.76: 74264 3.76 - 4.33: 99183 4.33 - 4.90: 161760 Nonbonded interactions: 379775 Sorted by model distance: nonbonded pdb=" O GLYAF 111 " pdb=" OG1 THRAF 115 " model vdw 2.056 3.040 nonbonded pdb=" O LYSBM 806 " pdb=" OH TYRBM 873 " model vdw 2.069 3.040 nonbonded pdb=" O ARGAE 16 " pdb=" OH TYRAF 94 " model vdw 2.070 3.040 nonbonded pdb=" OD2 ASPAH 100 " pdb=" OG1 THRAH 102 " model vdw 2.074 3.040 nonbonded pdb=" OD1 ASNAE 71 " pdb=" OG1 THRAE 121 " model vdw 2.080 3.040 ... (remaining 379770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'AA' selection = chain 'AC' selection = chain 'AE' selection = chain 'AH' selection = chain 'AJ' selection = chain 'AL' selection = chain 'AW' selection = chain 'AY' selection = chain 'BA' selection = chain 'BD' selection = chain 'BF' selection = chain 'BH' } ncs_group { reference = chain 'AB' selection = chain 'AD' selection = chain 'AF' selection = chain 'AI' selection = chain 'AK' selection = chain 'AM' selection = chain 'AX' selection = chain 'AZ' selection = chain 'BB' selection = chain 'BE' selection = chain 'BG' selection = chain 'BI' } ncs_group { reference = chain 'AO' selection = chain 'BK' } ncs_group { reference = chain 'AQ' selection = chain 'BM' } ncs_group { reference = chain 'AS' selection = chain 'BP' } ncs_group { reference = chain 'AT' selection = chain 'BO' } ncs_group { reference = chain 'AU' selection = chain 'AV' selection = chain 'BQ' selection = chain 'BR' } 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: 2.370 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: 0.040 Extract box with map and model: 1.830 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 93.240 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.480 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: 0.020 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.004 0.090 43584 Z= 0.288 Angle : 0.685 15.259 59090 Z= 0.343 Chirality : 0.039 0.226 6668 Planarity : 0.008 0.148 7602 Dihedral : 13.194 107.347 16836 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 38.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.94 % Rotamer: Outliers : 0.05 % Allowed : 0.36 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.12), residues: 5398 helix: 1.56 (0.08), residues: 3833 sheet: -0.58 (0.39), residues: 166 loop : -0.82 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAS 288 HIS 0.000 0.000 HISBM 807 PHE 0.018 0.001 PHEAU 203 TYR 0.035 0.001 TYRAX 73 ARG 0.007 0.000 ARGAH 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 758 time to evaluate : 5.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 MET cc_start: 0.7866 (mmm) cc_final: 0.7550 (mpp) REVERT: AB 161 SER cc_start: 0.8539 (t) cc_final: 0.8196 (p) REVERT: AC 27 LYS cc_start: 0.9127 (tppt) cc_final: 0.8896 (tppt) REVERT: AC 86 ASP cc_start: 0.8673 (t70) cc_final: 0.8457 (t70) REVERT: AD 28 LYS cc_start: 0.9053 (mtmm) cc_final: 0.8753 (mtmp) REVERT: AF 1 MET cc_start: 0.7588 (ppp) cc_final: 0.7259 (ppp) REVERT: AF 28 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8829 (mptm) REVERT: AH 6 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8398 (tmmt) REVERT: AJ 60 GLN cc_start: 0.7899 (mt0) cc_final: 0.7663 (tm-30) REVERT: AJ 77 MET cc_start: 0.6311 (mmp) cc_final: 0.5950 (mmt) REVERT: AK 17 LYS cc_start: 0.8371 (mptt) cc_final: 0.8120 (mmtt) REVERT: AK 28 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8573 (mtmp) REVERT: AS 201 TYR cc_start: 0.8035 (t80) cc_final: 0.7617 (t80) REVERT: AT 264 PHE cc_start: 0.6846 (m-10) cc_final: 0.6594 (m-80) REVERT: AT 272 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8442 (tppp) REVERT: AT 299 PHE cc_start: 0.7836 (t80) cc_final: 0.7335 (t80) REVERT: AW 77 MET cc_start: 0.8866 (mmt) cc_final: 0.8491 (mmp) REVERT: AY 73 TYR cc_start: 0.8164 (t80) cc_final: 0.7759 (t80) REVERT: AZ 82 ILE cc_start: 0.8587 (mm) cc_final: 0.8179 (mm) REVERT: BE 128 GLN cc_start: 0.8580 (tt0) cc_final: 0.8339 (tm-30) REVERT: BF 77 MET cc_start: 0.8637 (mmp) cc_final: 0.8410 (mmp) REVERT: BH 154 ASP cc_start: 0.8685 (m-30) cc_final: 0.8389 (m-30) REVERT: BO 243 GLU cc_start: 0.7771 (pt0) cc_final: 0.7556 (tm-30) REVERT: BO 244 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8045 (mm-30) REVERT: BO 268 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8357 (tppt) REVERT: BO 288 TRP cc_start: 0.7166 (m-90) cc_final: 0.6651 (m-90) REVERT: BO 293 ASN cc_start: 0.8757 (t0) cc_final: 0.8425 (t0) REVERT: BO 300 PHE cc_start: 0.8845 (t80) cc_final: 0.8571 (t80) REVERT: BR 241 ASN cc_start: 0.8821 (p0) cc_final: 0.8355 (p0) outliers start: 2 outliers final: 3 residues processed: 760 average time/residue: 1.7867 time to fit residues: 1638.0766 Evaluate side-chains 505 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 502 time to evaluate : 5.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AS residue 314 ASN Chi-restraints excluded: chain BE residue 44 ILE Chi-restraints excluded: chain BR residue 239 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 4.9990 chunk 409 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 423 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 315 optimal weight: 5.9990 chunk 490 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 2 GLN AD 128 GLN AE 53 GLN ** AF 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 128 GLN AH 71 ASN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 128 GLN AK 2 GLN AK 10 ASN ** AK 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 10 ASN AQ 769 ASN ** AS 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 274 GLN ** AT 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 10 ASN AZ 10 ASN BB 2 GLN BB 10 ASN ** BB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 131 GLN BF 71 ASN ** BG 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 71 ASN BM 865 ASN BO 208 ASN BO 236 ASN BO 247 ASN ** BP 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 150 GLN ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 43584 Z= 0.271 Angle : 0.721 11.580 59090 Z= 0.357 Chirality : 0.043 0.327 6668 Planarity : 0.005 0.071 7602 Dihedral : 8.593 93.002 7174 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 2.06 % Allowed : 12.84 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.11), residues: 5398 helix: 1.38 (0.08), residues: 3878 sheet: -0.97 (0.37), residues: 180 loop : -0.77 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPBP 41 HIS 0.002 0.001 HISAQ 807 PHE 0.020 0.002 PHEAU 203 TYR 0.026 0.002 TYRAJ 88 ARG 0.010 0.001 ARGBK 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 611 time to evaluate : 4.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 MET cc_start: 0.7761 (mmm) cc_final: 0.7283 (mpp) REVERT: AD 28 LYS cc_start: 0.9071 (mtmm) cc_final: 0.8731 (mtmp) REVERT: AD 54 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: AF 54 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: AF 135 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: AH 6 LYS cc_start: 0.8692 (tmtt) cc_final: 0.8349 (tmmt) REVERT: AJ 60 GLN cc_start: 0.7954 (mt0) cc_final: 0.7725 (tm-30) REVERT: AJ 85 MET cc_start: 0.5970 (OUTLIER) cc_final: 0.5709 (ttp) REVERT: AK 17 LYS cc_start: 0.8522 (mptt) cc_final: 0.8220 (mmtt) REVERT: AK 28 LYS cc_start: 0.8884 (mtmm) cc_final: 0.8631 (mtmp) REVERT: AQ 817 LYS cc_start: 0.8937 (tmtt) cc_final: 0.8701 (tptp) REVERT: AS 201 TYR cc_start: 0.7936 (t80) cc_final: 0.7685 (t80) REVERT: AT 281 ASN cc_start: 0.7405 (m-40) cc_final: 0.7190 (t0) REVERT: AT 299 PHE cc_start: 0.7870 (t80) cc_final: 0.7516 (t80) REVERT: AY 6 LYS cc_start: 0.9051 (tppp) cc_final: 0.8672 (tptp) REVERT: AY 10 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8670 (m-40) REVERT: AY 73 TYR cc_start: 0.8108 (t80) cc_final: 0.7588 (t80) REVERT: AZ 53 LYS cc_start: 0.9026 (tttt) cc_final: 0.8804 (tttm) REVERT: AZ 114 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: BA 6 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8465 (mtmt) REVERT: BD 6 LYS cc_start: 0.7993 (ptmt) cc_final: 0.7582 (ptpt) REVERT: BD 85 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6786 (mmm) REVERT: BD 160 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7657 (tmm) REVERT: BE 43 VAL cc_start: 0.9173 (t) cc_final: 0.8949 (p) REVERT: BF 77 MET cc_start: 0.8303 (mmp) cc_final: 0.8046 (mmp) REVERT: BG 147 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9026 (tppt) REVERT: BH 24 ASP cc_start: 0.8603 (m-30) cc_final: 0.8194 (p0) REVERT: BH 154 ASP cc_start: 0.8752 (m-30) cc_final: 0.8442 (m-30) REVERT: BI 58 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8450 (ptpp) REVERT: BO 243 GLU cc_start: 0.7896 (pt0) cc_final: 0.7364 (tm-30) REVERT: BO 268 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8388 (tppt) REVERT: BO 286 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7381 (tt) REVERT: BO 288 TRP cc_start: 0.7182 (m-90) cc_final: 0.6684 (m-90) REVERT: BO 293 ASN cc_start: 0.8649 (t0) cc_final: 0.8424 (t0) REVERT: BQ 241 ASN cc_start: 0.9146 (t0) cc_final: 0.8936 (t0) REVERT: BR 241 ASN cc_start: 0.8647 (p0) cc_final: 0.8209 (p0) outliers start: 91 outliers final: 23 residues processed: 658 average time/residue: 1.7380 time to fit residues: 1387.6226 Evaluate side-chains 537 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 503 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AB residue 14 VAL Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 61 LYS Chi-restraints excluded: chain AD residue 54 GLU Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AJ residue 8 ILE Chi-restraints excluded: chain AJ residue 78 THR Chi-restraints excluded: chain AJ residue 85 MET Chi-restraints excluded: chain AM residue 135 GLU Chi-restraints excluded: chain AO residue 53 VAL Chi-restraints excluded: chain AO residue 57 THR Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AW residue 24 ASP Chi-restraints excluded: chain AY residue 10 ASN Chi-restraints excluded: chain AZ residue 114 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 31 THR Chi-restraints excluded: chain BD residue 85 MET Chi-restraints excluded: chain BD residue 133 MET Chi-restraints excluded: chain BD residue 160 MET Chi-restraints excluded: chain BE residue 44 ILE Chi-restraints excluded: chain BF residue 60 GLN Chi-restraints excluded: chain BG residue 147 LYS Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BI residue 58 LYS Chi-restraints excluded: chain BM residue 710 SER Chi-restraints excluded: chain BO residue 211 ASP Chi-restraints excluded: chain BO residue 286 ILE Chi-restraints excluded: chain BO residue 304 ASP Chi-restraints excluded: chain BP residue 21 VAL Chi-restraints excluded: chain BP residue 74 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 408 optimal weight: 4.9990 chunk 333 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 491 optimal weight: 8.9990 chunk 530 optimal weight: 0.1980 chunk 437 optimal weight: 0.9980 chunk 487 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 128 GLN AF 71 ASN AH 10 ASN AH 128 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 71 ASN ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 13 GLN BP 143 GLN BP 293 ASN BQ 217 ASN ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 43584 Z= 0.241 Angle : 0.680 10.783 59090 Z= 0.338 Chirality : 0.041 0.264 6668 Planarity : 0.005 0.051 7602 Dihedral : 8.502 95.703 7170 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.68 % Rotamer: Outliers : 2.75 % Allowed : 15.79 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.11), residues: 5398 helix: 1.38 (0.08), residues: 3866 sheet: -1.23 (0.38), residues: 184 loop : -0.75 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAT 288 HIS 0.002 0.001 HISAQ 807 PHE 0.017 0.001 PHEAU 203 TYR 0.026 0.001 TYRAJ 88 ARG 0.010 0.000 ARGBK 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 573 time to evaluate : 4.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 77 MET cc_start: 0.7390 (mmm) cc_final: 0.7044 (mpp) REVERT: AB 54 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: AC 107 ILE cc_start: 0.9309 (mm) cc_final: 0.9085 (mm) REVERT: AD 28 LYS cc_start: 0.9116 (mtmm) cc_final: 0.8730 (mtmp) REVERT: AF 135 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: AH 6 LYS cc_start: 0.8728 (tmtt) cc_final: 0.8369 (tmmt) REVERT: AH 60 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: AJ 60 GLN cc_start: 0.7935 (mt0) cc_final: 0.7680 (tm-30) REVERT: AK 17 LYS cc_start: 0.8542 (mptt) cc_final: 0.8250 (mmtt) REVERT: AK 28 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8612 (mtmp) REVERT: AQ 817 LYS cc_start: 0.8943 (tmtt) cc_final: 0.8716 (tptp) REVERT: AS 284 MET cc_start: 0.5734 (tpt) cc_final: 0.5376 (tpt) REVERT: AT 264 PHE cc_start: 0.6057 (m-80) cc_final: 0.5796 (m-80) REVERT: AT 284 MET cc_start: 0.6586 (mmm) cc_final: 0.6310 (mmt) REVERT: AT 304 ASP cc_start: 0.8173 (m-30) cc_final: 0.7693 (p0) REVERT: AW 60 GLN cc_start: 0.8241 (mp10) cc_final: 0.7823 (mp10) REVERT: AW 64 ASP cc_start: 0.8762 (p0) cc_final: 0.8491 (p0) REVERT: AW 133 MET cc_start: 0.8993 (mtp) cc_final: 0.8758 (mtt) REVERT: AX 54 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: AX 147 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8934 (ttpp) REVERT: AY 73 TYR cc_start: 0.8083 (t80) cc_final: 0.7581 (t80) REVERT: AZ 28 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8752 (mtmt) REVERT: AZ 106 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: AZ 114 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: BA 6 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8473 (mtmt) REVERT: BD 6 LYS cc_start: 0.7896 (ptmt) cc_final: 0.7585 (ptpp) REVERT: BG 147 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9026 (tppt) REVERT: BH 154 ASP cc_start: 0.8758 (m-30) cc_final: 0.8443 (m-30) REVERT: BI 58 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8514 (ptpp) REVERT: BO 243 GLU cc_start: 0.7883 (pt0) cc_final: 0.7348 (tm-30) REVERT: BO 244 GLU cc_start: 0.8662 (mm-30) cc_final: 0.7347 (mm-30) REVERT: BO 288 TRP cc_start: 0.7048 (m-90) cc_final: 0.6805 (m-90) REVERT: BO 300 PHE cc_start: 0.9032 (t80) cc_final: 0.8832 (t80) REVERT: BR 241 ASN cc_start: 0.8570 (p0) cc_final: 0.8157 (p0) outliers start: 121 outliers final: 36 residues processed: 642 average time/residue: 1.7588 time to fit residues: 1368.6663 Evaluate side-chains 547 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 502 time to evaluate : 5.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AB residue 54 GLU Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AD residue 54 GLU Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AH residue 60 GLN Chi-restraints excluded: chain AJ residue 8 ILE Chi-restraints excluded: chain AJ residue 53 GLN Chi-restraints excluded: chain AM residue 121 VAL Chi-restraints excluded: chain AM residue 135 GLU Chi-restraints excluded: chain AO residue 53 VAL Chi-restraints excluded: chain AO residue 57 THR Chi-restraints excluded: chain AQ residue 726 LEU Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 92 THR Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AX residue 54 GLU Chi-restraints excluded: chain AX residue 147 LYS Chi-restraints excluded: chain AY residue 41 GLU Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 72 MET Chi-restraints excluded: chain AZ residue 106 GLU Chi-restraints excluded: chain AZ residue 114 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BF residue 60 GLN Chi-restraints excluded: chain BG residue 106 GLU Chi-restraints excluded: chain BG residue 147 LYS Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BH residue 97 VAL Chi-restraints excluded: chain BH residue 133 MET Chi-restraints excluded: chain BH residue 141 MET Chi-restraints excluded: chain BI residue 58 LYS Chi-restraints excluded: chain BK residue 7 THR Chi-restraints excluded: chain BK residue 66 LEU Chi-restraints excluded: chain BM residue 700 ILE Chi-restraints excluded: chain BO residue 211 ASP Chi-restraints excluded: chain BO residue 304 ASP Chi-restraints excluded: chain BP residue 21 VAL Chi-restraints excluded: chain BP residue 70 GLU Chi-restraints excluded: chain BQ residue 224 SER Chi-restraints excluded: chain BQ residue 241 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 0.9980 chunk 369 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 493 optimal weight: 4.9990 chunk 521 optimal weight: 0.8980 chunk 257 optimal weight: 8.9990 chunk 467 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 128 GLN AH 10 ASN AI 15 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 128 GLN ** AK 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 117 ASN ** BG 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 43584 Z= 0.243 Angle : 0.681 11.665 59090 Z= 0.337 Chirality : 0.041 0.292 6668 Planarity : 0.004 0.055 7602 Dihedral : 8.384 95.200 7168 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Rotamer: Outliers : 3.36 % Allowed : 17.85 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.11), residues: 5398 helix: 1.39 (0.08), residues: 3870 sheet: -1.19 (0.38), residues: 184 loop : -0.79 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAT 288 HIS 0.002 0.001 HISAQ 807 PHE 0.025 0.001 PHEAU 203 TYR 0.025 0.001 TYRAE 73 ARG 0.012 0.000 ARGBK 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 559 time to evaluate : 4.679 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: AA 77 MET cc_start: 0.7445 (mmm) cc_final: 0.7088 (mpp) REVERT: AB 54 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: AC 27 LYS cc_start: 0.9204 (tppt) cc_final: 0.8884 (tptt) REVERT: AC 107 ILE cc_start: 0.9313 (mm) cc_final: 0.9087 (mt) REVERT: AC 123 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.9011 (pp) REVERT: AD 28 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8833 (mtmp) REVERT: AF 135 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: AH 6 LYS cc_start: 0.8752 (tmtt) cc_final: 0.8386 (tmmt) REVERT: AH 60 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: AH 87 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: AJ 8 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9269 (mt) REVERT: AJ 60 GLN cc_start: 0.7918 (mt0) cc_final: 0.7670 (tm-30) REVERT: AK 17 LYS cc_start: 0.8558 (mptt) cc_final: 0.8247 (mmtt) REVERT: AK 28 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8681 (mtmm) REVERT: AL 6 LYS cc_start: 0.8811 (mtmp) cc_final: 0.8560 (mttp) REVERT: AQ 817 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8716 (tptp) REVERT: AS 29 SER cc_start: 0.8009 (OUTLIER) cc_final: 0.7808 (p) REVERT: AT 235 GLU cc_start: 0.8167 (mp0) cc_final: 0.7937 (tp30) REVERT: AT 284 MET cc_start: 0.6700 (mmm) cc_final: 0.6458 (mmm) REVERT: AT 289 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7417 (ttt180) REVERT: AT 304 ASP cc_start: 0.8126 (m-30) cc_final: 0.7753 (p0) REVERT: AW 60 GLN cc_start: 0.8314 (mp10) cc_final: 0.7875 (mp10) REVERT: AW 64 ASP cc_start: 0.8751 (p0) cc_final: 0.8471 (p0) REVERT: AW 133 MET cc_start: 0.9017 (mtp) cc_final: 0.8773 (mtt) REVERT: AX 54 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: AX 147 LYS cc_start: 0.9234 (ttmm) cc_final: 0.8973 (ttpp) REVERT: AY 73 TYR cc_start: 0.8043 (t80) cc_final: 0.7549 (t80) REVERT: AY 88 TYR cc_start: 0.7878 (m-80) cc_final: 0.7658 (m-80) REVERT: AZ 106 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: AZ 114 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: BA 6 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8514 (mtmt) REVERT: BB 1 MET cc_start: 0.8060 (tmm) cc_final: 0.7846 (ttt) REVERT: BD 6 LYS cc_start: 0.7913 (ptmt) cc_final: 0.7609 (ptpp) REVERT: BD 160 MET cc_start: 0.7681 (tmm) cc_final: 0.7466 (tmm) REVERT: BE 100 ASP cc_start: 0.6783 (m-30) cc_final: 0.6384 (p0) REVERT: BG 1 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7519 (ptm) REVERT: BG 147 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.9029 (tppt) REVERT: BH 24 ASP cc_start: 0.8636 (m-30) cc_final: 0.8169 (p0) REVERT: BH 154 ASP cc_start: 0.8749 (m-30) cc_final: 0.8426 (m-30) REVERT: BM 880 ASP cc_start: 0.8471 (t0) cc_final: 0.8247 (t0) REVERT: BO 242 ARG cc_start: 0.8956 (ptp-110) cc_final: 0.8711 (ptp90) REVERT: BO 243 GLU cc_start: 0.7850 (pt0) cc_final: 0.7321 (tm-30) REVERT: BO 268 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7775 (tppt) REVERT: BO 288 TRP cc_start: 0.7288 (m-90) cc_final: 0.6941 (m-90) REVERT: BO 300 PHE cc_start: 0.8992 (t80) cc_final: 0.8744 (t80) REVERT: BR 209 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8311 (ttpp) REVERT: BR 241 ASN cc_start: 0.8548 (p0) cc_final: 0.8157 (p0) outliers start: 148 outliers final: 44 residues processed: 651 average time/residue: 1.7257 time to fit residues: 1372.7033 Evaluate side-chains 552 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 495 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 14 VAL Chi-restraints excluded: chain AB residue 54 GLU Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 61 LYS Chi-restraints excluded: chain AC residue 123 ILE Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AH residue 60 GLN Chi-restraints excluded: chain AH residue 87 TYR Chi-restraints excluded: chain AI residue 87 TYR Chi-restraints excluded: chain AI residue 97 LEU Chi-restraints excluded: chain AI residue 126 THR Chi-restraints excluded: chain AJ residue 8 ILE Chi-restraints excluded: chain AJ residue 53 GLN Chi-restraints excluded: chain AM residue 121 VAL Chi-restraints excluded: chain AM residue 135 GLU Chi-restraints excluded: chain AO residue 53 VAL Chi-restraints excluded: chain AO residue 57 THR Chi-restraints excluded: chain AQ residue 726 LEU Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 29 SER Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 92 THR Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 218 THR Chi-restraints excluded: chain AT residue 289 ARG Chi-restraints excluded: chain AT residue 293 ASN Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AX residue 54 GLU Chi-restraints excluded: chain AY residue 53 GLN Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 106 GLU Chi-restraints excluded: chain AZ residue 114 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BE residue 14 VAL Chi-restraints excluded: chain BG residue 1 MET Chi-restraints excluded: chain BG residue 106 GLU Chi-restraints excluded: chain BG residue 108 VAL Chi-restraints excluded: chain BG residue 147 LYS Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BH residue 30 VAL Chi-restraints excluded: chain BH residue 53 GLN Chi-restraints excluded: chain BH residue 97 VAL Chi-restraints excluded: chain BH residue 141 MET Chi-restraints excluded: chain BK residue 7 THR Chi-restraints excluded: chain BK residue 66 LEU Chi-restraints excluded: chain BM residue 700 ILE Chi-restraints excluded: chain BO residue 304 ASP Chi-restraints excluded: chain BP residue 21 VAL Chi-restraints excluded: chain BP residue 70 GLU Chi-restraints excluded: chain BQ residue 224 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 445 optimal weight: 0.6980 chunk 360 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 468 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 128 GLN AH 10 ASN AI 15 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 131 GLN ** AS 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 246 GLN ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 2 GLN ** BG 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 43584 Z= 0.214 Angle : 0.679 12.012 59090 Z= 0.335 Chirality : 0.041 0.244 6668 Planarity : 0.004 0.061 7602 Dihedral : 8.370 94.222 7168 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.68 % Rotamer: Outliers : 3.22 % Allowed : 19.44 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.11), residues: 5398 helix: 1.43 (0.08), residues: 3872 sheet: -0.77 (0.39), residues: 174 loop : -0.85 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPAT 288 HIS 0.002 0.001 HISAQ 807 PHE 0.021 0.001 PHEAU 203 TYR 0.025 0.001 TYRAE 73 ARG 0.014 0.000 ARGBK 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 562 time to evaluate : 5.010 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: AA 77 MET cc_start: 0.7427 (mmm) cc_final: 0.7090 (mpp) REVERT: AC 77 MET cc_start: 0.8213 (mmp) cc_final: 0.7983 (mmp) REVERT: AC 107 ILE cc_start: 0.9305 (mm) cc_final: 0.9087 (mt) REVERT: AC 123 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9043 (pp) REVERT: AD 149 MET cc_start: 0.8883 (mmm) cc_final: 0.8579 (tpt) REVERT: AF 54 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: AF 135 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: AH 6 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8350 (tmmt) REVERT: AH 60 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8538 (pm20) REVERT: AJ 8 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9234 (mt) REVERT: AJ 60 GLN cc_start: 0.7945 (mt0) cc_final: 0.7627 (tm-30) REVERT: AK 17 LYS cc_start: 0.8605 (mptt) cc_final: 0.8291 (mmtt) REVERT: AK 28 LYS cc_start: 0.8924 (mtmm) cc_final: 0.8605 (mtmp) REVERT: AQ 817 LYS cc_start: 0.8952 (tmtt) cc_final: 0.8701 (tptp) REVERT: AS 29 SER cc_start: 0.8043 (OUTLIER) cc_final: 0.7720 (p) REVERT: AT 235 GLU cc_start: 0.8129 (mp0) cc_final: 0.7902 (tp30) REVERT: AT 284 MET cc_start: 0.6640 (mmm) cc_final: 0.6290 (mmm) REVERT: AT 304 ASP cc_start: 0.8134 (m-30) cc_final: 0.7727 (p0) REVERT: AW 60 GLN cc_start: 0.8349 (mp10) cc_final: 0.7945 (mp10) REVERT: AW 64 ASP cc_start: 0.8696 (p0) cc_final: 0.8360 (p0) REVERT: AX 28 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8186 (mmmt) REVERT: AX 54 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: AX 147 LYS cc_start: 0.9227 (ttmm) cc_final: 0.8975 (ttpp) REVERT: AY 73 TYR cc_start: 0.7989 (t80) cc_final: 0.7519 (t80) REVERT: AZ 97 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8858 (tt) REVERT: AZ 106 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: AZ 114 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: BA 141 MET cc_start: 0.8875 (ttm) cc_final: 0.8646 (tmm) REVERT: BD 6 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7616 (ptpp) REVERT: BD 73 TYR cc_start: 0.6681 (t80) cc_final: 0.6469 (t80) REVERT: BD 160 MET cc_start: 0.7601 (tmm) cc_final: 0.7326 (tmm) REVERT: BE 43 VAL cc_start: 0.9241 (t) cc_final: 0.8991 (p) REVERT: BE 100 ASP cc_start: 0.6710 (m-30) cc_final: 0.6455 (p0) REVERT: BG 1 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7543 (ptm) REVERT: BG 147 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8996 (tppt) REVERT: BH 154 ASP cc_start: 0.8751 (m-30) cc_final: 0.8433 (m-30) REVERT: BI 58 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8397 (ptpp) REVERT: BI 128 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8969 (mp10) REVERT: BO 268 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7770 (tppt) REVERT: BO 288 TRP cc_start: 0.7334 (m-90) cc_final: 0.7016 (m-90) REVERT: BO 300 PHE cc_start: 0.8958 (t80) cc_final: 0.8738 (t80) REVERT: BR 241 ASN cc_start: 0.8518 (p0) cc_final: 0.8160 (p0) outliers start: 142 outliers final: 49 residues processed: 650 average time/residue: 1.7249 time to fit residues: 1367.5545 Evaluate side-chains 567 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 504 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 4 VAL Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 123 ILE Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AH residue 60 GLN Chi-restraints excluded: chain AI residue 97 LEU Chi-restraints excluded: chain AJ residue 8 ILE Chi-restraints excluded: chain AK residue 5 ILE Chi-restraints excluded: chain AM residue 121 VAL Chi-restraints excluded: chain AM residue 135 GLU Chi-restraints excluded: chain AM residue 137 THR Chi-restraints excluded: chain AO residue 53 VAL Chi-restraints excluded: chain AO residue 57 THR Chi-restraints excluded: chain AQ residue 698 SER Chi-restraints excluded: chain AQ residue 726 LEU Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 29 SER Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 92 THR Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 293 ASN Chi-restraints excluded: chain AU residue 235 VAL Chi-restraints excluded: chain AV residue 219 LEU Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AW residue 24 ASP Chi-restraints excluded: chain AX residue 54 GLU Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AX residue 149 MET Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AY residue 159 LYS Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 72 MET Chi-restraints excluded: chain AZ residue 97 LEU Chi-restraints excluded: chain AZ residue 106 GLU Chi-restraints excluded: chain AZ residue 114 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BD residue 97 VAL Chi-restraints excluded: chain BD residue 133 MET Chi-restraints excluded: chain BG residue 1 MET Chi-restraints excluded: chain BG residue 106 GLU Chi-restraints excluded: chain BG residue 147 LYS Chi-restraints excluded: chain BH residue 30 VAL Chi-restraints excluded: chain BH residue 53 GLN Chi-restraints excluded: chain BH residue 97 VAL Chi-restraints excluded: chain BI residue 58 LYS Chi-restraints excluded: chain BI residue 128 GLN Chi-restraints excluded: chain BK residue 7 THR Chi-restraints excluded: chain BK residue 66 LEU Chi-restraints excluded: chain BM residue 700 ILE Chi-restraints excluded: chain BO residue 211 ASP Chi-restraints excluded: chain BO residue 304 ASP Chi-restraints excluded: chain BP residue 21 VAL Chi-restraints excluded: chain BP residue 70 GLU Chi-restraints excluded: chain BR residue 204 ILE Chi-restraints excluded: chain BR residue 221 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 4.9990 chunk 470 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 522 optimal weight: 10.0000 chunk 433 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 2 GLN AD 15 GLN AD 128 GLN AI 15 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 53 GLN ** AK 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 71 ASN ** AS 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 274 GLN ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 43584 Z= 0.293 Angle : 0.712 13.263 59090 Z= 0.351 Chirality : 0.042 0.232 6668 Planarity : 0.005 0.050 7602 Dihedral : 8.371 97.024 7168 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.55 % Rotamer: Outliers : 3.29 % Allowed : 20.21 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.11), residues: 5398 helix: 1.41 (0.08), residues: 3874 sheet: -0.85 (0.38), residues: 178 loop : -0.84 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPAT 288 HIS 0.002 0.001 HISBM 807 PHE 0.019 0.001 PHEAV 203 TYR 0.027 0.002 TYRAE 73 ARG 0.011 0.000 ARGBE 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 539 time to evaluate : 5.162 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: AA 77 MET cc_start: 0.7498 (mmm) cc_final: 0.7120 (mpp) REVERT: AC 107 ILE cc_start: 0.9308 (mm) cc_final: 0.9081 (mt) REVERT: AC 123 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9059 (pp) REVERT: AD 149 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8575 (tpt) REVERT: AF 135 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: AH 6 LYS cc_start: 0.8753 (tmtt) cc_final: 0.8325 (tmmt) REVERT: AH 60 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8526 (pm20) REVERT: AH 87 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.6901 (m-10) REVERT: AJ 60 GLN cc_start: 0.8024 (mt0) cc_final: 0.7696 (tm-30) REVERT: AK 17 LYS cc_start: 0.8595 (mptt) cc_final: 0.8295 (mmtt) REVERT: AK 28 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8624 (mtmp) REVERT: AQ 817 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8724 (tptp) REVERT: AS 29 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7640 (p) REVERT: AT 235 GLU cc_start: 0.8063 (mp0) cc_final: 0.7809 (tp30) REVERT: AT 284 MET cc_start: 0.6524 (mmm) cc_final: 0.6163 (mmm) REVERT: AT 304 ASP cc_start: 0.8160 (m-30) cc_final: 0.7875 (p0) REVERT: AW 60 GLN cc_start: 0.8334 (mp10) cc_final: 0.7936 (mp10) REVERT: AW 64 ASP cc_start: 0.8765 (p0) cc_final: 0.8469 (p0) REVERT: AW 115 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7558 (ttp) REVERT: AW 133 MET cc_start: 0.8982 (mtp) cc_final: 0.8705 (mtt) REVERT: AX 1 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6730 (ptm) REVERT: AX 54 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: AX 147 LYS cc_start: 0.9248 (ttmm) cc_final: 0.8999 (ttpp) REVERT: AY 53 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: AY 73 TYR cc_start: 0.8095 (t80) cc_final: 0.7551 (t80) REVERT: AY 88 TYR cc_start: 0.7922 (m-80) cc_final: 0.7645 (m-80) REVERT: AZ 97 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8913 (tt) REVERT: AZ 106 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: AZ 114 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: BD 6 LYS cc_start: 0.7966 (ptmt) cc_final: 0.7608 (ptpp) REVERT: BD 133 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6435 (mmm) REVERT: BD 160 MET cc_start: 0.7640 (tmm) cc_final: 0.7334 (tmm) REVERT: BE 26 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8301 (ptpt) REVERT: BE 43 VAL cc_start: 0.9228 (t) cc_final: 0.8991 (p) REVERT: BE 100 ASP cc_start: 0.6843 (m-30) cc_final: 0.6527 (p0) REVERT: BG 147 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9038 (tppt) REVERT: BH 24 ASP cc_start: 0.8577 (m-30) cc_final: 0.8148 (p0) REVERT: BH 154 ASP cc_start: 0.8763 (m-30) cc_final: 0.8449 (m-30) REVERT: BI 113 LYS cc_start: 0.8748 (tppp) cc_final: 0.8527 (tmmt) REVERT: BO 288 TRP cc_start: 0.7461 (m-90) cc_final: 0.7087 (m-90) REVERT: BO 300 PHE cc_start: 0.8974 (t80) cc_final: 0.8748 (t80) REVERT: BQ 223 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8494 (mpp80) REVERT: BR 241 ASN cc_start: 0.8467 (p0) cc_final: 0.8111 (p0) outliers start: 145 outliers final: 60 residues processed: 628 average time/residue: 1.7191 time to fit residues: 1324.3576 Evaluate side-chains 575 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 498 time to evaluate : 5.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AA residue 19 SER Chi-restraints excluded: chain AA residue 81 CYS Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 14 VAL Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 4 VAL Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 61 LYS Chi-restraints excluded: chain AC residue 123 ILE Chi-restraints excluded: chain AD residue 149 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 108 VAL Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AH residue 60 GLN Chi-restraints excluded: chain AH residue 87 TYR Chi-restraints excluded: chain AI residue 126 THR Chi-restraints excluded: chain AJ residue 65 ILE Chi-restraints excluded: chain AJ residue 78 THR Chi-restraints excluded: chain AK residue 5 ILE Chi-restraints excluded: chain AM residue 135 GLU Chi-restraints excluded: chain AM residue 137 THR Chi-restraints excluded: chain AO residue 53 VAL Chi-restraints excluded: chain AO residue 57 THR Chi-restraints excluded: chain AQ residue 698 SER Chi-restraints excluded: chain AQ residue 726 LEU Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 29 SER Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 74 MET Chi-restraints excluded: chain AS residue 92 THR Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 218 THR Chi-restraints excluded: chain AT residue 286 ILE Chi-restraints excluded: chain AT residue 293 ASN Chi-restraints excluded: chain AU residue 235 VAL Chi-restraints excluded: chain AV residue 219 LEU Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AW residue 24 ASP Chi-restraints excluded: chain AW residue 115 MET Chi-restraints excluded: chain AX residue 1 MET Chi-restraints excluded: chain AX residue 54 GLU Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AX residue 149 MET Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 53 GLN Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 72 MET Chi-restraints excluded: chain AZ residue 97 LEU Chi-restraints excluded: chain AZ residue 106 GLU Chi-restraints excluded: chain AZ residue 114 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 31 THR Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BD residue 97 VAL Chi-restraints excluded: chain BD residue 133 MET Chi-restraints excluded: chain BE residue 26 LYS Chi-restraints excluded: chain BG residue 108 VAL Chi-restraints excluded: chain BG residue 147 LYS Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BH residue 30 VAL Chi-restraints excluded: chain BH residue 81 CYS Chi-restraints excluded: chain BH residue 97 VAL Chi-restraints excluded: chain BK residue 7 THR Chi-restraints excluded: chain BK residue 53 VAL Chi-restraints excluded: chain BK residue 66 LEU Chi-restraints excluded: chain BM residue 700 ILE Chi-restraints excluded: chain BO residue 304 ASP Chi-restraints excluded: chain BP residue 74 MET Chi-restraints excluded: chain BQ residue 223 ARG Chi-restraints excluded: chain BQ residue 224 SER Chi-restraints excluded: chain BR residue 221 MET Chi-restraints excluded: chain BR residue 239 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 297 optimal weight: 0.0370 chunk 381 optimal weight: 3.9990 chunk 295 optimal weight: 0.7980 chunk 439 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 520 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 15 GLN AD 128 GLN AI 15 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 281 ASN ** BO 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 43584 Z= 0.220 Angle : 0.705 13.584 59090 Z= 0.347 Chirality : 0.041 0.228 6668 Planarity : 0.004 0.078 7602 Dihedral : 8.347 94.702 7168 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.24 % Favored : 96.65 % Rotamer: Outliers : 2.75 % Allowed : 21.44 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 5398 helix: 1.40 (0.08), residues: 3872 sheet: -0.71 (0.39), residues: 174 loop : -0.86 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPAT 288 HIS 0.001 0.000 HISBM 807 PHE 0.026 0.001 PHEAU 203 TYR 0.028 0.001 TYRAE 73 ARG 0.015 0.000 ARGBK 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 560 time to evaluate : 4.607 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: AA 77 MET cc_start: 0.7371 (mmm) cc_final: 0.7045 (mpp) REVERT: AA 132 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7085 (mm-30) REVERT: AC 107 ILE cc_start: 0.9289 (mm) cc_final: 0.9049 (mt) REVERT: AC 123 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9031 (pp) REVERT: AD 15 GLN cc_start: 0.8821 (mt0) cc_final: 0.8601 (mt0) REVERT: AD 17 LYS cc_start: 0.9061 (ptpp) cc_final: 0.8747 (ptpp) REVERT: AD 149 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8615 (tpt) REVERT: AE 160 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8375 (ttp) REVERT: AF 128 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: AF 135 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: AH 6 LYS cc_start: 0.8734 (tmtt) cc_final: 0.8314 (tmmt) REVERT: AH 60 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: AJ 60 GLN cc_start: 0.7957 (mt0) cc_final: 0.7620 (tm-30) REVERT: AK 17 LYS cc_start: 0.8574 (mptt) cc_final: 0.8276 (mmtt) REVERT: AK 28 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8616 (mtmp) REVERT: AM 135 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: AM 161 SER cc_start: 0.8424 (m) cc_final: 0.8122 (p) REVERT: AQ 817 LYS cc_start: 0.8967 (tmtt) cc_final: 0.8716 (tptp) REVERT: AS 29 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7590 (p) REVERT: AS 61 MET cc_start: 0.6903 (tpt) cc_final: 0.6592 (tpt) REVERT: AT 235 GLU cc_start: 0.7985 (mp0) cc_final: 0.7723 (tp30) REVERT: AT 284 MET cc_start: 0.6507 (mmm) cc_final: 0.6214 (mmm) REVERT: AT 297 LYS cc_start: 0.8453 (mmmm) cc_final: 0.8083 (mmmm) REVERT: AT 304 ASP cc_start: 0.8154 (m-30) cc_final: 0.7866 (p0) REVERT: AW 60 GLN cc_start: 0.8320 (mp10) cc_final: 0.7959 (mp10) REVERT: AW 64 ASP cc_start: 0.8661 (p0) cc_final: 0.8330 (p0) REVERT: AW 114 GLU cc_start: 0.8350 (mp0) cc_final: 0.8139 (mp0) REVERT: AW 115 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7540 (ttp) REVERT: AX 1 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6544 (ptm) REVERT: AX 28 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8189 (mmmt) REVERT: AX 54 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: AX 147 LYS cc_start: 0.9247 (ttmm) cc_final: 0.9004 (ttpp) REVERT: AY 53 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: AY 73 TYR cc_start: 0.8004 (t80) cc_final: 0.7566 (t80) REVERT: AY 77 MET cc_start: 0.6838 (mmp) cc_final: 0.6281 (mmp) REVERT: AY 100 ASP cc_start: 0.7744 (p0) cc_final: 0.7492 (p0) REVERT: AZ 106 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: AZ 114 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: AZ 149 MET cc_start: 0.9261 (mmm) cc_final: 0.8973 (tpt) REVERT: BA 6 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8256 (mttp) REVERT: BA 141 MET cc_start: 0.8854 (ttm) cc_final: 0.8624 (tmm) REVERT: BD 6 LYS cc_start: 0.7954 (ptmt) cc_final: 0.7589 (ptpp) REVERT: BD 73 TYR cc_start: 0.6736 (t80) cc_final: 0.6497 (t80) REVERT: BE 84 ASP cc_start: 0.7685 (m-30) cc_final: 0.7455 (m-30) REVERT: BE 86 ASP cc_start: 0.7895 (m-30) cc_final: 0.7506 (m-30) REVERT: BE 144 ASP cc_start: 0.8632 (p0) cc_final: 0.8379 (p0) REVERT: BG 74 THR cc_start: 0.8790 (p) cc_final: 0.8587 (t) REVERT: BG 147 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8998 (tppt) REVERT: BH 24 ASP cc_start: 0.8555 (m-30) cc_final: 0.8259 (p0) REVERT: BH 154 ASP cc_start: 0.8732 (m-30) cc_final: 0.8410 (m-30) REVERT: BI 54 GLU cc_start: 0.7876 (pm20) cc_final: 0.7101 (pm20) REVERT: BI 83 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: BO 242 ARG cc_start: 0.8955 (ptp-110) cc_final: 0.8676 (ptp90) REVERT: BO 288 TRP cc_start: 0.7378 (m-90) cc_final: 0.7107 (m-90) REVERT: BO 300 PHE cc_start: 0.8950 (t80) cc_final: 0.8665 (t80) REVERT: BP 313 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8069 (pp) REVERT: BQ 223 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8467 (mpp80) REVERT: BR 241 ASN cc_start: 0.8470 (p0) cc_final: 0.8177 (p0) outliers start: 121 outliers final: 46 residues processed: 640 average time/residue: 1.6770 time to fit residues: 1310.1450 Evaluate side-chains 577 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 513 time to evaluate : 5.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AA residue 19 SER Chi-restraints excluded: chain AA residue 81 CYS Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AC residue 4 VAL Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 61 LYS Chi-restraints excluded: chain AC residue 123 ILE Chi-restraints excluded: chain AD residue 149 MET Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 128 GLN Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AH residue 60 GLN Chi-restraints excluded: chain AJ residue 129 SER Chi-restraints excluded: chain AM residue 135 GLU Chi-restraints excluded: chain AO residue 53 VAL Chi-restraints excluded: chain AO residue 57 THR Chi-restraints excluded: chain AQ residue 698 SER Chi-restraints excluded: chain AQ residue 726 LEU Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 29 SER Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 71 ILE Chi-restraints excluded: chain AS residue 92 THR Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 218 THR Chi-restraints excluded: chain AU residue 235 VAL Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AW residue 24 ASP Chi-restraints excluded: chain AW residue 115 MET Chi-restraints excluded: chain AX residue 1 MET Chi-restraints excluded: chain AX residue 54 GLU Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AX residue 149 MET Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 53 GLN Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 106 GLU Chi-restraints excluded: chain AZ residue 114 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BD residue 97 VAL Chi-restraints excluded: chain BG residue 108 VAL Chi-restraints excluded: chain BG residue 147 LYS Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BH residue 30 VAL Chi-restraints excluded: chain BH residue 81 CYS Chi-restraints excluded: chain BI residue 15 GLN Chi-restraints excluded: chain BI residue 83 ARG Chi-restraints excluded: chain BK residue 7 THR Chi-restraints excluded: chain BK residue 53 VAL Chi-restraints excluded: chain BK residue 66 LEU Chi-restraints excluded: chain BM residue 700 ILE Chi-restraints excluded: chain BO residue 211 ASP Chi-restraints excluded: chain BO residue 214 ILE Chi-restraints excluded: chain BP residue 313 LEU Chi-restraints excluded: chain BQ residue 223 ARG Chi-restraints excluded: chain BQ residue 224 SER Chi-restraints excluded: chain BR residue 221 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 102 optimal weight: 0.0060 chunk 100 optimal weight: 0.9980 chunk 330 optimal weight: 0.8980 chunk 354 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 409 optimal weight: 7.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 128 GLN AI 15 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 10 ASN ** AK 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 266 GLN ** BO 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 62 GLN ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 43584 Z= 0.213 Angle : 0.721 14.194 59090 Z= 0.354 Chirality : 0.041 0.220 6668 Planarity : 0.004 0.058 7602 Dihedral : 8.342 94.534 7168 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.24 % Favored : 96.65 % Rotamer: Outliers : 2.45 % Allowed : 22.44 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 5398 helix: 1.41 (0.08), residues: 3884 sheet: -0.62 (0.39), residues: 174 loop : -0.90 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRPAT 288 HIS 0.001 0.001 HISAQ 807 PHE 0.027 0.001 PHEAU 203 TYR 0.028 0.001 TYRAE 73 ARG 0.014 0.000 ARGAO 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 558 time to evaluate : 4.976 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: AA 77 MET cc_start: 0.7382 (mmm) cc_final: 0.7053 (mpp) REVERT: AA 132 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6856 (mm-30) REVERT: AC 123 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.9025 (pp) REVERT: AD 15 GLN cc_start: 0.8841 (mt0) cc_final: 0.8545 (mt0) REVERT: AD 17 LYS cc_start: 0.9029 (ptpp) cc_final: 0.8815 (ptpp) REVERT: AD 149 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8600 (tpt) REVERT: AE 160 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8345 (ttp) REVERT: AF 128 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8246 (mp10) REVERT: AF 135 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: AH 6 LYS cc_start: 0.8758 (tmtt) cc_final: 0.8357 (tmmt) REVERT: AH 60 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: AI 152 TYR cc_start: 0.7142 (m-10) cc_final: 0.6906 (m-10) REVERT: AJ 60 GLN cc_start: 0.8153 (mt0) cc_final: 0.7630 (tm-30) REVERT: AK 17 LYS cc_start: 0.8564 (mptt) cc_final: 0.8305 (mmtt) REVERT: AK 28 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8588 (mtmp) REVERT: AK 148 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7866 (mt-10) REVERT: AM 161 SER cc_start: 0.8426 (m) cc_final: 0.8118 (p) REVERT: AQ 817 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8733 (tptp) REVERT: AS 29 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7630 (p) REVERT: AT 284 MET cc_start: 0.6539 (mmm) cc_final: 0.6227 (mmm) REVERT: AT 288 TRP cc_start: 0.7748 (m-90) cc_final: 0.7433 (m-90) REVERT: AT 304 ASP cc_start: 0.8126 (m-30) cc_final: 0.7870 (p0) REVERT: AW 64 ASP cc_start: 0.8655 (p0) cc_final: 0.8333 (p0) REVERT: AX 1 MET cc_start: 0.6951 (ptt) cc_final: 0.6537 (ptm) REVERT: AX 28 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8152 (mmmt) REVERT: AX 54 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: AX 147 LYS cc_start: 0.9237 (ttmm) cc_final: 0.8995 (ttpp) REVERT: AY 53 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: AY 73 TYR cc_start: 0.8002 (t80) cc_final: 0.7524 (t80) REVERT: AZ 106 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: AZ 114 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: BA 6 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8290 (mttp) REVERT: BA 141 MET cc_start: 0.8800 (ttm) cc_final: 0.8580 (tmm) REVERT: BD 6 LYS cc_start: 0.7926 (ptmt) cc_final: 0.7564 (ptpp) REVERT: BG 74 THR cc_start: 0.8765 (p) cc_final: 0.8560 (t) REVERT: BG 147 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8976 (tppt) REVERT: BH 24 ASP cc_start: 0.8551 (m-30) cc_final: 0.8250 (p0) REVERT: BH 154 ASP cc_start: 0.8719 (m-30) cc_final: 0.8394 (m-30) REVERT: BI 24 MET cc_start: 0.8812 (tpp) cc_final: 0.8421 (mpp) REVERT: BI 54 GLU cc_start: 0.7868 (pm20) cc_final: 0.7131 (pm20) REVERT: BO 300 PHE cc_start: 0.8961 (t80) cc_final: 0.8676 (t80) REVERT: BP 313 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8030 (pp) REVERT: BR 241 ASN cc_start: 0.8245 (p0) cc_final: 0.7964 (p0) outliers start: 108 outliers final: 48 residues processed: 631 average time/residue: 1.7095 time to fit residues: 1313.1827 Evaluate side-chains 576 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 515 time to evaluate : 5.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AA residue 81 CYS Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 4 VAL Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 123 ILE Chi-restraints excluded: chain AD residue 149 MET Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 108 VAL Chi-restraints excluded: chain AF residue 128 GLN Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AH residue 60 GLN Chi-restraints excluded: chain AI residue 97 LEU Chi-restraints excluded: chain AO residue 53 VAL Chi-restraints excluded: chain AO residue 57 THR Chi-restraints excluded: chain AQ residue 698 SER Chi-restraints excluded: chain AQ residue 726 LEU Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 29 SER Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 92 THR Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AU residue 235 VAL Chi-restraints excluded: chain AV residue 219 LEU Chi-restraints excluded: chain AW residue 24 ASP Chi-restraints excluded: chain AX residue 54 GLU Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AX residue 149 MET Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 53 GLN Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 106 GLU Chi-restraints excluded: chain AZ residue 114 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BD residue 50 ILE Chi-restraints excluded: chain BD residue 97 VAL Chi-restraints excluded: chain BF residue 49 THR Chi-restraints excluded: chain BF residue 81 CYS Chi-restraints excluded: chain BF residue 102 THR Chi-restraints excluded: chain BG residue 108 VAL Chi-restraints excluded: chain BG residue 147 LYS Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BH residue 81 CYS Chi-restraints excluded: chain BI residue 15 GLN Chi-restraints excluded: chain BK residue 7 THR Chi-restraints excluded: chain BK residue 53 VAL Chi-restraints excluded: chain BK residue 66 LEU Chi-restraints excluded: chain BM residue 700 ILE Chi-restraints excluded: chain BO residue 211 ASP Chi-restraints excluded: chain BO residue 214 ILE Chi-restraints excluded: chain BO residue 304 ASP Chi-restraints excluded: chain BP residue 313 LEU Chi-restraints excluded: chain BQ residue 224 SER Chi-restraints excluded: chain BR residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 0.8980 chunk 498 optimal weight: 9.9990 chunk 454 optimal weight: 5.9990 chunk 485 optimal weight: 0.6980 chunk 291 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 380 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 438 optimal weight: 4.9990 chunk 458 optimal weight: 1.9990 chunk 483 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 71 ASN AD 128 GLN AI 15 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 35 ASN ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 824 GLN BO 281 ASN ** BO 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 62 GLN ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 43584 Z= 0.223 Angle : 0.738 15.474 59090 Z= 0.364 Chirality : 0.041 0.241 6668 Planarity : 0.005 0.089 7602 Dihedral : 8.345 94.678 7168 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 2.04 % Allowed : 23.28 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 5398 helix: 1.40 (0.08), residues: 3872 sheet: -0.58 (0.39), residues: 174 loop : -0.88 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRPBO 288 HIS 0.001 0.001 HISAQ 807 PHE 0.025 0.001 PHEAU 203 TYR 0.029 0.001 TYRAE 73 ARG 0.018 0.000 ARGBK 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 539 time to evaluate : 4.921 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: AA 77 MET cc_start: 0.7352 (mmm) cc_final: 0.7054 (mpp) REVERT: AA 132 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6837 (mm-30) REVERT: AA 141 MET cc_start: 0.7361 (ttp) cc_final: 0.6997 (pp-130) REVERT: AC 123 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.9025 (pp) REVERT: AD 149 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8606 (tpt) REVERT: AE 160 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8364 (ttp) REVERT: AF 135 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: AH 6 LYS cc_start: 0.8764 (tmtt) cc_final: 0.8360 (tmmt) REVERT: AI 17 LYS cc_start: 0.8441 (mtmm) cc_final: 0.8216 (mtmm) REVERT: AJ 60 GLN cc_start: 0.8153 (mt0) cc_final: 0.7636 (tm-30) REVERT: AK 17 LYS cc_start: 0.8573 (mptt) cc_final: 0.8309 (mmtt) REVERT: AK 28 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8572 (mtmp) REVERT: AK 148 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7862 (mt-10) REVERT: AM 161 SER cc_start: 0.8487 (m) cc_final: 0.8193 (p) REVERT: AQ 817 LYS cc_start: 0.8954 (tmtt) cc_final: 0.8735 (tptp) REVERT: AS 29 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7684 (p) REVERT: AT 284 MET cc_start: 0.6528 (mmm) cc_final: 0.6191 (mmm) REVERT: AT 304 ASP cc_start: 0.8111 (m-30) cc_final: 0.7891 (p0) REVERT: AW 60 GLN cc_start: 0.8292 (mp10) cc_final: 0.7966 (mp10) REVERT: AW 64 ASP cc_start: 0.8673 (p0) cc_final: 0.8387 (p0) REVERT: AW 141 MET cc_start: 0.7319 (ttm) cc_final: 0.7028 (tmm) REVERT: AX 1 MET cc_start: 0.6921 (ptt) cc_final: 0.6550 (ptm) REVERT: AX 28 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8165 (mmmt) REVERT: AX 54 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: AX 147 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8998 (ttpp) REVERT: AY 53 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8448 (pm20) REVERT: AY 73 TYR cc_start: 0.8031 (t80) cc_final: 0.7589 (t80) REVERT: AZ 28 LYS cc_start: 0.8977 (mtmm) cc_final: 0.8635 (mptt) REVERT: AZ 106 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: AZ 149 MET cc_start: 0.9242 (mmm) cc_final: 0.9035 (tpt) REVERT: BA 6 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8292 (mttp) REVERT: BA 141 MET cc_start: 0.8771 (ttm) cc_final: 0.8552 (tmm) REVERT: BD 6 LYS cc_start: 0.7949 (ptmt) cc_final: 0.7585 (ptpp) REVERT: BF 64 ASP cc_start: 0.7989 (m-30) cc_final: 0.7750 (m-30) REVERT: BG 74 THR cc_start: 0.8765 (p) cc_final: 0.8558 (t) REVERT: BH 24 ASP cc_start: 0.8551 (m-30) cc_final: 0.8249 (p0) REVERT: BH 154 ASP cc_start: 0.8711 (m-30) cc_final: 0.8386 (m-30) REVERT: BI 24 MET cc_start: 0.8796 (tpp) cc_final: 0.8387 (mpp) REVERT: BI 54 GLU cc_start: 0.7894 (pm20) cc_final: 0.7160 (pm20) REVERT: BO 214 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8786 (pp) REVERT: BO 300 PHE cc_start: 0.8948 (t80) cc_final: 0.8606 (t80) REVERT: BP 313 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7993 (pp) outliers start: 90 outliers final: 52 residues processed: 600 average time/residue: 1.7232 time to fit residues: 1260.1161 Evaluate side-chains 575 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 513 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AA residue 81 CYS Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 4 VAL Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 123 ILE Chi-restraints excluded: chain AD residue 149 MET Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 108 VAL Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AI residue 61 LEU Chi-restraints excluded: chain AI residue 72 MET Chi-restraints excluded: chain AJ residue 6 LYS Chi-restraints excluded: chain AJ residue 144 ASP Chi-restraints excluded: chain AO residue 53 VAL Chi-restraints excluded: chain AO residue 57 THR Chi-restraints excluded: chain AQ residue 698 SER Chi-restraints excluded: chain AQ residue 726 LEU Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 29 SER Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 92 THR Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AU residue 235 VAL Chi-restraints excluded: chain AV residue 219 LEU Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AW residue 24 ASP Chi-restraints excluded: chain AX residue 54 GLU Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AX residue 149 MET Chi-restraints excluded: chain AX residue 156 ILE Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 53 GLN Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 106 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BD residue 50 ILE Chi-restraints excluded: chain BD residue 97 VAL Chi-restraints excluded: chain BF residue 49 THR Chi-restraints excluded: chain BF residue 81 CYS Chi-restraints excluded: chain BF residue 102 THR Chi-restraints excluded: chain BG residue 108 VAL Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BH residue 30 VAL Chi-restraints excluded: chain BH residue 81 CYS Chi-restraints excluded: chain BI residue 15 GLN Chi-restraints excluded: chain BK residue 7 THR Chi-restraints excluded: chain BK residue 53 VAL Chi-restraints excluded: chain BK residue 66 LEU Chi-restraints excluded: chain BO residue 214 ILE Chi-restraints excluded: chain BO residue 304 ASP Chi-restraints excluded: chain BP residue 313 LEU Chi-restraints excluded: chain BQ residue 224 SER Chi-restraints excluded: chain BR residue 204 ILE Chi-restraints excluded: chain BR residue 239 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 1.9990 chunk 512 optimal weight: 0.0970 chunk 313 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 356 optimal weight: 0.9990 chunk 537 optimal weight: 0.5980 chunk 495 optimal weight: 40.0000 chunk 428 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 262 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 15 GLN AD 128 GLN AI 15 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 2 GLN AZ 2 GLN ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 62 GLN ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 43584 Z= 0.217 Angle : 0.756 15.265 59090 Z= 0.374 Chirality : 0.041 0.231 6668 Planarity : 0.005 0.067 7602 Dihedral : 8.365 94.132 7168 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Rotamer: Outliers : 1.70 % Allowed : 23.93 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.11), residues: 5398 helix: 1.37 (0.08), residues: 3884 sheet: -0.40 (0.40), residues: 170 loop : -0.91 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRPBO 288 HIS 0.001 0.001 HISBM 807 PHE 0.042 0.001 PHEAB 31 TYR 0.038 0.001 TYRAB 73 ARG 0.019 0.000 ARGBO 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10796 Ramachandran restraints generated. 5398 Oldfield, 0 Emsley, 5398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 544 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 132 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6788 (mm-30) REVERT: AC 123 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9015 (pp) REVERT: AD 149 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8603 (tpt) REVERT: AE 160 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8348 (ttp) REVERT: AF 135 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: AH 6 LYS cc_start: 0.8769 (tmtt) cc_final: 0.8365 (tmmt) REVERT: AI 152 TYR cc_start: 0.7401 (m-10) cc_final: 0.7155 (m-10) REVERT: AJ 60 GLN cc_start: 0.8095 (mt0) cc_final: 0.7589 (tm-30) REVERT: AK 17 LYS cc_start: 0.8561 (mptt) cc_final: 0.8305 (mmtt) REVERT: AK 28 LYS cc_start: 0.8890 (mtmm) cc_final: 0.8559 (mtmp) REVERT: AK 148 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7840 (mt-10) REVERT: AM 161 SER cc_start: 0.8499 (m) cc_final: 0.8213 (p) REVERT: AQ 817 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8735 (tptp) REVERT: AS 29 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7708 (p) REVERT: AT 284 MET cc_start: 0.6609 (mmm) cc_final: 0.6258 (mmm) REVERT: AT 288 TRP cc_start: 0.7793 (m-90) cc_final: 0.7581 (m-90) REVERT: AW 60 GLN cc_start: 0.8284 (mp10) cc_final: 0.7961 (mp10) REVERT: AW 64 ASP cc_start: 0.8707 (p0) cc_final: 0.8410 (p0) REVERT: AX 1 MET cc_start: 0.6847 (ptt) cc_final: 0.6441 (ptm) REVERT: AX 54 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: AX 147 LYS cc_start: 0.9236 (ttmm) cc_final: 0.9000 (ttpp) REVERT: AY 73 TYR cc_start: 0.7978 (t80) cc_final: 0.7629 (t80) REVERT: AY 77 MET cc_start: 0.6872 (mmp) cc_final: 0.6549 (mmp) REVERT: AZ 106 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: BA 6 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8266 (mttp) REVERT: BA 141 MET cc_start: 0.8736 (ttm) cc_final: 0.8525 (tmm) REVERT: BD 6 LYS cc_start: 0.7891 (ptmt) cc_final: 0.7536 (ptpp) REVERT: BD 160 MET cc_start: 0.7688 (tmm) cc_final: 0.7385 (tmm) REVERT: BF 64 ASP cc_start: 0.8058 (m-30) cc_final: 0.7833 (m-30) REVERT: BG 74 THR cc_start: 0.8760 (p) cc_final: 0.8552 (t) REVERT: BH 24 ASP cc_start: 0.8549 (m-30) cc_final: 0.8242 (p0) REVERT: BH 154 ASP cc_start: 0.8715 (m-30) cc_final: 0.8387 (m-30) REVERT: BI 15 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8195 (mp10) REVERT: BI 24 MET cc_start: 0.8793 (tpp) cc_final: 0.8406 (mpp) REVERT: BI 54 GLU cc_start: 0.7884 (pm20) cc_final: 0.7058 (pm20) REVERT: BO 214 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8768 (pp) REVERT: BO 300 PHE cc_start: 0.8960 (t80) cc_final: 0.8599 (t80) REVERT: BP 313 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7949 (pp) outliers start: 75 outliers final: 49 residues processed: 593 average time/residue: 1.6852 time to fit residues: 1223.1322 Evaluate side-chains 572 residues out of total 4408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 513 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AA residue 81 CYS Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 4 VAL Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 123 ILE Chi-restraints excluded: chain AD residue 149 MET Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 108 VAL Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AI residue 72 MET Chi-restraints excluded: chain AJ residue 129 SER Chi-restraints excluded: chain AJ residue 144 ASP Chi-restraints excluded: chain AO residue 53 VAL Chi-restraints excluded: chain AO residue 57 THR Chi-restraints excluded: chain AQ residue 726 LEU Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 29 SER Chi-restraints excluded: chain AS residue 92 THR Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AU residue 235 VAL Chi-restraints excluded: chain AV residue 219 LEU Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AX residue 54 GLU Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AX residue 156 ILE Chi-restraints excluded: chain AY residue 17 TYR Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 53 GLN Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 106 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BD residue 50 ILE Chi-restraints excluded: chain BD residue 97 VAL Chi-restraints excluded: chain BF residue 49 THR Chi-restraints excluded: chain BF residue 81 CYS Chi-restraints excluded: chain BF residue 102 THR Chi-restraints excluded: chain BG residue 108 VAL Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BH residue 30 VAL Chi-restraints excluded: chain BH residue 81 CYS Chi-restraints excluded: chain BI residue 15 GLN Chi-restraints excluded: chain BI residue 128 GLN Chi-restraints excluded: chain BK residue 7 THR Chi-restraints excluded: chain BK residue 53 VAL Chi-restraints excluded: chain BK residue 66 LEU Chi-restraints excluded: chain BO residue 214 ILE Chi-restraints excluded: chain BO residue 304 ASP Chi-restraints excluded: chain BP residue 313 LEU Chi-restraints excluded: chain BQ residue 224 SER Chi-restraints excluded: chain BR residue 204 ILE Chi-restraints excluded: chain BR residue 239 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 0.0050 chunk 456 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 395 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 429 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 440 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 71 ASN ** AB 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 128 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 117 ASN AO 35 ASN ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 53 GLN ** BO 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 206 ASN ** BO 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 62 GLN ** BR 230 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 = 0.3530 r_free = 0.3530 target = 0.059860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.046120 restraints weight = 169453.663| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.00 r_work: 0.3039 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43584 Z= 0.227 Angle : 0.760 16.395 59090 Z= 0.376 Chirality : 0.041 0.217 6668 Planarity : 0.005 0.107 7602 Dihedral : 8.354 93.873 7168 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.48 % Rotamer: Outliers : 1.79 % Allowed : 23.96 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.11), residues: 5398 helix: 1.35 (0.08), residues: 3896 sheet: -0.41 (0.41), residues: 154 loop : -0.94 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRPBO 288 HIS 0.001 0.001 HISAQ 807 PHE 0.021 0.001 PHEAU 203 TYR 0.029 0.001 TYRAE 73 ARG 0.019 0.000 ARGBK 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18381.11 seconds wall clock time: 332 minutes 18.24 seconds (19938.24 seconds total)