Starting phenix.real_space_refine on Sat Feb 24 09:10:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scc_25033/02_2024/7scc_25033_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scc_25033/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scc_25033/02_2024/7scc_25033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scc_25033/02_2024/7scc_25033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scc_25033/02_2024/7scc_25033_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scc_25033/02_2024/7scc_25033_trim_updated.pdb" } 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 Residue "AQ PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 22.40, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.96 Conformation dependent library (CDL) restraints added in 7.8 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... running ksdssp... Secondary structure from input PDB file: 264 helices and 8 sheets defined 66.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.16 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 14 Processing helix chain 'AA' and resid 20 through 31 Processing helix chain 'AA' and resid 33 through 45 Processing helix chain 'AA' and resid 47 through 61 Processing helix chain 'AA' and resid 63 through 66 Processing helix chain 'AA' and resid 75 through 96 removed outlier: 3.878A pdb=" N CYSAA 81 " --> pdb=" O METAA 77 " (cutoff:3.500A) Processing helix chain 'AA' and resid 102 through 107 Processing helix chain 'AA' and resid 112 through 119 Processing helix chain 'AA' and resid 123 through 140 Processing helix chain 'AA' and resid 143 through 160 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 4 through 14 Processing helix chain 'AB' and resid 21 through 59 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 75 through 98 Processing helix chain 'AB' and resid 102 through 107 Processing helix chain 'AB' and resid 112 through 119 Processing helix chain 'AB' and resid 123 through 141 Processing helix chain 'AB' and resid 143 through 160 removed outlier: 3.623A pdb=" N TYRAB 152 " --> pdb=" O GLUAB 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 3 through 14 Processing helix chain 'AC' and resid 20 through 45 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) Processing helix chain 'AC' and resid 47 through 61 Processing helix chain 'AC' and resid 63 through 66 No H-bonds generated for 'chain 'AC' and resid 63 through 66' Processing helix chain 'AC' and resid 77 through 98 Processing helix chain 'AC' and resid 102 through 108 Processing helix chain 'AC' and resid 112 through 117 Processing helix chain 'AC' and resid 123 through 140 Processing helix chain 'AC' and resid 144 through 160 removed outlier: 3.953A pdb=" N TYRAC 152 " --> pdb=" O GLUAC 148 " (cutoff:3.500A) Processing helix chain 'AD' and resid 4 through 14 Processing helix chain 'AD' and resid 21 through 46 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) Processing helix chain 'AD' and resid 48 through 57 Processing helix chain 'AD' and resid 75 through 98 Processing helix chain 'AD' and resid 103 through 107 Processing helix chain 'AD' and resid 112 through 119 Processing helix chain 'AD' and resid 123 through 141 Processing helix chain 'AD' and resid 144 through 160 removed outlier: 3.674A pdb=" N TYRAD 152 " --> pdb=" O GLUAD 148 " (cutoff:3.500A) Processing helix chain 'AE' and resid 3 through 14 Processing helix chain 'AE' and resid 20 through 45 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) Processing helix chain 'AE' and resid 47 through 61 Processing helix chain 'AE' and resid 63 through 66 No H-bonds generated for 'chain 'AE' and resid 63 through 66' Processing helix chain 'AE' and resid 75 through 98 Processing helix chain 'AE' and resid 102 through 108 Processing helix chain 'AE' and resid 112 through 119 Processing helix chain 'AE' and resid 123 through 139 Processing helix chain 'AE' and resid 143 through 160 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 4 through 14 Processing helix chain 'AF' and resid 21 through 59 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 75 through 98 Processing helix chain 'AF' and resid 102 through 107 Processing helix chain 'AF' and resid 113 through 119 Processing helix chain 'AF' and resid 123 through 141 Processing helix chain 'AF' and resid 143 through 160 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 20 through 61 removed outlier: 4.984A pdb=" N ALAAH 34 " --> pdb=" O VALAH 30 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ALAAH 35 " --> pdb=" O THRAH 31 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SERAH 46 " --> pdb=" O THRAH 42 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARGAH 47 " --> pdb=" O LEUAH 43 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLUAH 48 " --> pdb=" O THRAH 44 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THRAH 49 " --> pdb=" O GLYAH 45 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLNAH 60 " --> pdb=" O ASPAH 56 " (cutoff:3.500A) Processing helix chain 'AH' and resid 63 through 65 No H-bonds generated for 'chain 'AH' and resid 63 through 65' Processing helix chain 'AH' and resid 75 through 98 Processing helix chain 'AH' and resid 102 through 108 Processing helix chain 'AH' and resid 112 through 118 Processing helix chain 'AH' and resid 123 through 139 Processing helix chain 'AH' and resid 143 through 160 removed outlier: 3.819A pdb=" N TYRAH 152 " --> pdb=" O GLUAH 148 " (cutoff:3.500A) Processing helix chain 'AI' and resid 4 through 14 Processing helix chain 'AI' and resid 21 through 46 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) Processing helix chain 'AI' and resid 48 through 58 removed outlier: 4.094A pdb=" N VALAI 52 " --> pdb=" O ALAAI 48 " (cutoff:3.500A) Processing helix chain 'AI' and resid 74 through 98 Processing helix chain 'AI' and resid 102 through 107 Processing helix chain 'AI' and resid 112 through 119 Processing helix chain 'AI' and resid 123 through 141 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 144 through 160 Processing helix chain 'AJ' and resid 3 through 14 removed outlier: 3.515A pdb=" N GLUAJ 14 " --> pdb=" O ASNAJ 10 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 20 through 45 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 47 through 61 Processing helix chain 'AJ' and resid 63 through 65 No H-bonds generated for 'chain 'AJ' and resid 63 through 65' Processing helix chain 'AJ' and resid 75 through 98 Processing helix chain 'AJ' and resid 101 through 108 removed outlier: 4.472A pdb=" N GLYAJ 108 " --> pdb=" O GLUAJ 105 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 112 through 118 Processing helix chain 'AJ' and resid 123 through 139 Processing helix chain 'AJ' and resid 143 through 160 removed outlier: 4.231A pdb=" N TYRAJ 152 " --> pdb=" O GLUAJ 148 " (cutoff:3.500A) Processing helix chain 'AK' and resid 4 through 14 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) Processing helix chain 'AK' and resid 21 through 46 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 48 through 59 Processing helix chain 'AK' and resid 76 through 98 Processing helix chain 'AK' and resid 104 through 107 No H-bonds generated for 'chain 'AK' and resid 104 through 107' Processing helix chain 'AK' and resid 112 through 119 Processing helix chain 'AK' and resid 123 through 141 Processing helix chain 'AK' and resid 144 through 160 Processing helix chain 'AL' and resid 3 through 14 Processing helix chain 'AL' and resid 20 through 45 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) Processing helix chain 'AL' and resid 47 through 61 Processing helix chain 'AL' and resid 63 through 66 No H-bonds generated for 'chain 'AL' and resid 63 through 66' Processing helix chain 'AL' and resid 75 through 98 Processing helix chain 'AL' and resid 102 through 108 Processing helix chain 'AL' and resid 112 through 119 Processing helix chain 'AL' and resid 123 through 139 Processing helix chain 'AL' and resid 143 through 160 removed outlier: 4.033A pdb=" N TYRAL 152 " --> pdb=" O GLUAL 148 " (cutoff:3.500A) Processing helix chain 'AM' and resid 4 through 14 Processing helix chain 'AM' and resid 21 through 57 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 74 through 98 Processing helix chain 'AM' and resid 102 through 107 removed outlier: 3.543A pdb=" N GLUAM 106 " --> pdb=" O SERAM 102 " (cutoff:3.500A) Processing helix chain 'AM' and resid 112 through 119 Processing helix chain 'AM' and resid 123 through 141 Processing helix chain 'AM' and resid 144 through 160 removed outlier: 3.771A pdb=" N TYRAM 152 " --> pdb=" O GLUAM 148 " (cutoff:3.500A) Processing helix chain 'AO' and resid 22 through 25 No H-bonds generated for 'chain 'AO' and resid 22 through 25' Processing helix chain 'AO' and resid 33 through 45 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 690 through 695 Processing helix chain 'AQ' and resid 703 through 710 Processing helix chain 'AQ' and resid 716 through 718 No H-bonds generated for 'chain 'AQ' and resid 716 through 718' Processing helix chain 'AQ' and resid 732 through 747 Processing helix chain 'AQ' and resid 761 through 768 Processing helix chain 'AQ' and resid 774 through 782 Processing helix chain 'AQ' and resid 785 through 790 Processing helix chain 'AQ' and resid 797 through 807 Processing helix chain 'AQ' and resid 816 through 828 Processing helix chain 'AQ' and resid 830 through 839 removed outlier: 3.552A pdb=" N PHEAQ 834 " --> pdb=" O GLYAQ 830 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 842 through 848 Processing helix chain 'AQ' and resid 865 through 873 Processing helix chain 'AS' and resid 20 through 30 removed outlier: 3.579A pdb=" N GLNAS 30 " --> pdb=" O ALAAS 26 " (cutoff:3.500A) Processing helix chain 'AS' and resid 33 through 46 Processing helix chain 'AS' and resid 56 through 58 No H-bonds generated for 'chain 'AS' and resid 56 through 58' Processing helix chain 'AS' and resid 61 through 63 No H-bonds generated for 'chain 'AS' and resid 61 through 63' Processing helix chain 'AS' and resid 65 through 73 Processing helix chain 'AS' and resid 76 through 87 Processing helix chain 'AS' and resid 93 through 99 Processing helix chain 'AS' and resid 103 through 119 Processing helix chain 'AS' and resid 133 through 144 Processing helix chain 'AS' and resid 147 through 159 Processing helix chain 'AS' and resid 196 through 206 removed outlier: 3.745A pdb=" N ASNAS 206 " --> pdb=" O METAS 202 " (cutoff:3.500A) Processing helix chain 'AS' and resid 210 through 214 Processing helix chain 'AS' and resid 234 through 243 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 196 through 207 Processing helix chain 'AT' and resid 210 through 216 removed outlier: 4.349A pdb=" N GLUAT 215 " --> pdb=" O ASPAT 211 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEUAT 216 " --> pdb=" O THRAT 212 " (cutoff:3.500A) Processing helix chain 'AT' and resid 234 through 243 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 225 removed outlier: 5.102A pdb=" N GLYAU 220 " --> pdb=" O ASNAU 217 " (cutoff:3.500A) Processing helix chain 'AV' and resid 215 through 225 removed outlier: 5.094A pdb=" N GLYAV 220 " --> pdb=" O ASNAV 217 " (cutoff:3.500A) Processing helix chain 'AW' and resid 3 through 14 Processing helix chain 'AW' and resid 20 through 45 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) Processing helix chain 'AW' and resid 47 through 61 Processing helix chain 'AW' and resid 63 through 66 No H-bonds generated for 'chain 'AW' and resid 63 through 66' Processing helix chain 'AW' and resid 75 through 98 Processing helix chain 'AW' and resid 102 through 108 Processing helix chain 'AW' and resid 112 through 119 Processing helix chain 'AW' and resid 123 through 139 Processing helix chain 'AW' and resid 143 through 160 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 6 through 14 Processing helix chain 'AX' and resid 21 through 46 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) Processing helix chain 'AX' and resid 48 through 59 removed outlier: 4.134A pdb=" N VALAX 52 " --> pdb=" O ALAAX 48 " (cutoff:3.500A) Processing helix chain 'AX' and resid 75 through 98 Processing helix chain 'AX' and resid 102 through 107 Processing helix chain 'AX' and resid 112 through 119 Processing helix chain 'AX' and resid 123 through 141 Processing helix chain 'AX' and resid 143 through 160 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 20 through 45 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 47 through 61 Processing helix chain 'AY' and resid 77 through 98 Processing helix chain 'AY' and resid 102 through 108 Processing helix chain 'AY' and resid 112 through 117 Processing helix chain 'AY' and resid 123 through 140 Processing helix chain 'AY' and resid 144 through 160 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 4 through 13 Processing helix chain 'AZ' and resid 21 through 59 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) removed outlier: 6.139A pdb=" N ALAAZ 49 " --> pdb=" O SERAZ 45 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THRAZ 50 " --> pdb=" O ALAAZ 46 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 75 through 98 Processing helix chain 'AZ' and resid 103 through 107 Processing helix chain 'AZ' and resid 112 through 119 Processing helix chain 'AZ' and resid 123 through 141 Processing helix chain 'AZ' and resid 144 through 160 removed outlier: 3.589A pdb=" N TYRAZ 152 " --> pdb=" O GLUAZ 148 " (cutoff:3.500A) Processing helix chain 'BA' and resid 3 through 14 Processing helix chain 'BA' and resid 20 through 45 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) Processing helix chain 'BA' and resid 47 through 61 Processing helix chain 'BA' and resid 63 through 66 No H-bonds generated for 'chain 'BA' and resid 63 through 66' Processing helix chain 'BA' and resid 75 through 98 Processing helix chain 'BA' and resid 102 through 108 Processing helix chain 'BA' and resid 112 through 119 Processing helix chain 'BA' and resid 123 through 139 Processing helix chain 'BA' and resid 143 through 160 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 4 through 14 Processing helix chain 'BB' and resid 21 through 46 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 48 through 59 Processing helix chain 'BB' and resid 75 through 98 Processing helix chain 'BB' and resid 102 through 107 Processing helix chain 'BB' and resid 112 through 119 Processing helix chain 'BB' and resid 123 through 160 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 13 Processing helix chain 'BD' and resid 20 through 45 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 47 through 61 Processing helix chain 'BD' and resid 63 through 65 No H-bonds generated for 'chain 'BD' and resid 63 through 65' Processing helix chain 'BD' and resid 75 through 98 removed outlier: 3.572A pdb=" N ALABD 79 " --> pdb=" O GLUBD 75 " (cutoff:3.500A) Processing helix chain 'BD' and resid 102 through 108 Processing helix chain 'BD' and resid 112 through 119 Processing helix chain 'BD' and resid 123 through 140 Processing helix chain 'BD' and resid 143 through 160 removed outlier: 3.658A pdb=" N GLUBD 148 " --> pdb=" O ASPBD 144 " (cutoff:3.500A) Processing helix chain 'BE' and resid 4 through 14 Processing helix chain 'BE' and resid 21 through 46 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) Processing helix chain 'BE' and resid 48 through 58 removed outlier: 4.216A pdb=" N VALBE 52 " --> pdb=" O ALABE 48 " (cutoff:3.500A) Processing helix chain 'BE' and resid 75 through 98 Processing helix chain 'BE' and resid 101 through 107 Processing helix chain 'BE' and resid 112 through 119 Processing helix chain 'BE' and resid 123 through 141 Processing helix chain 'BE' and resid 144 through 160 Processing helix chain 'BF' and resid 3 through 14 Processing helix chain 'BF' and resid 20 through 45 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 47 through 61 Processing helix chain 'BF' and resid 63 through 66 No H-bonds generated for 'chain 'BF' and resid 63 through 66' Processing helix chain 'BF' and resid 75 through 98 Processing helix chain 'BF' and resid 102 through 108 Processing helix chain 'BF' and resid 112 through 119 Processing helix chain 'BF' and resid 123 through 140 Processing helix chain 'BF' and resid 143 through 160 removed outlier: 4.031A pdb=" N TYRBF 152 " --> pdb=" O GLUBF 148 " (cutoff:3.500A) Processing helix chain 'BG' and resid 4 through 14 Processing helix chain 'BG' and resid 21 through 46 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 48 through 57 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 76 through 98 Processing helix chain 'BG' and resid 103 through 107 Processing helix chain 'BG' and resid 112 through 119 Processing helix chain 'BG' and resid 123 through 138 Processing helix chain 'BG' and resid 143 through 160 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 14 Processing helix chain 'BH' and resid 20 through 61 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) removed outlier: 3.666A pdb=" N ARGBH 47 " --> pdb=" O LEUBH 43 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLUBH 48 " --> pdb=" O THRBH 44 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THRBH 49 " --> pdb=" O GLYBH 45 " (cutoff:3.500A) Processing helix chain 'BH' and resid 63 through 66 No H-bonds generated for 'chain 'BH' and resid 63 through 66' Processing helix chain 'BH' and resid 75 through 98 Processing helix chain 'BH' and resid 102 through 108 Processing helix chain 'BH' and resid 112 through 119 Processing helix chain 'BH' and resid 123 through 140 removed outlier: 3.635A pdb=" N LEUBH 140 " --> pdb=" O VALBH 136 " (cutoff:3.500A) Processing helix chain 'BH' and resid 143 through 160 removed outlier: 3.986A pdb=" N TYRBH 152 " --> pdb=" O GLUBH 148 " (cutoff:3.500A) Processing helix chain 'BI' and resid 4 through 14 Processing helix chain 'BI' and resid 21 through 46 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) Processing helix chain 'BI' and resid 48 through 57 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 75 through 98 Processing helix chain 'BI' and resid 102 through 107 removed outlier: 3.665A pdb=" N GLUBI 106 " --> pdb=" O SERBI 102 " (cutoff:3.500A) Processing helix chain 'BI' and resid 112 through 119 Processing helix chain 'BI' and resid 123 through 141 removed outlier: 3.534A pdb=" N LEUBI 140 " --> pdb=" O VALBI 136 " (cutoff:3.500A) Processing helix chain 'BI' and resid 144 through 160 removed outlier: 3.537A pdb=" N TYRBI 152 " --> pdb=" O GLUBI 148 " (cutoff:3.500A) Processing helix chain 'BK' and resid 33 through 45 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 690 through 695 Processing helix chain 'BM' and resid 703 through 710 Processing helix chain 'BM' and resid 716 through 718 No H-bonds generated for 'chain 'BM' and resid 716 through 718' Processing helix chain 'BM' and resid 732 through 746 Processing helix chain 'BM' and resid 761 through 768 Processing helix chain 'BM' and resid 774 through 782 Processing helix chain 'BM' and resid 785 through 791 Processing helix chain 'BM' and resid 797 through 807 Processing helix chain 'BM' and resid 816 through 829 Processing helix chain 'BM' and resid 832 through 840 Processing helix chain 'BM' and resid 842 through 847 Processing helix chain 'BM' and resid 865 through 873 Processing helix chain 'BO' and resid 196 through 207 Processing helix chain 'BO' and resid 210 through 216 removed outlier: 4.291A pdb=" N GLUBO 215 " --> pdb=" O ASPBO 211 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEUBO 216 " --> pdb=" O THRBO 212 " (cutoff:3.500A) Processing helix chain 'BO' and resid 234 through 243 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 18 through 30 removed outlier: 4.544A pdb=" N VALBP 21 " --> pdb=" O ALABP 18 " (cutoff:3.500A) Proline residue: BP 22 - end of helix removed outlier: 3.868A pdb=" N GLNBP 30 " --> pdb=" O ARGBP 27 " (cutoff:3.500A) Processing helix chain 'BP' and resid 33 through 45 Processing helix chain 'BP' and resid 56 through 58 No H-bonds generated for 'chain 'BP' and resid 56 through 58' Processing helix chain 'BP' and resid 61 through 63 No H-bonds generated for 'chain 'BP' and resid 61 through 63' Processing helix chain 'BP' and resid 65 through 73 Processing helix chain 'BP' and resid 76 through 88 Processing helix chain 'BP' and resid 93 through 99 Processing helix chain 'BP' and resid 103 through 119 Processing helix chain 'BP' and resid 133 through 144 Processing helix chain 'BP' and resid 147 through 159 Processing helix chain 'BP' and resid 196 through 206 removed outlier: 3.568A pdb=" N ASNBP 206 " --> pdb=" O METBP 202 " (cutoff:3.500A) Processing helix chain 'BP' and resid 210 through 216 removed outlier: 3.708A pdb=" N GLUBP 215 " --> pdb=" O ASPBP 211 " (cutoff:3.500A) Processing helix chain 'BP' and resid 234 through 243 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 225 removed outlier: 5.280A pdb=" N GLYBQ 220 " --> pdb=" O ASNBQ 217 " (cutoff:3.500A) Processing helix chain 'BR' and resid 215 through 225 removed outlier: 4.788A pdb=" N GLYBR 220 " --> pdb=" O ASNBR 217 " (cutoff:3.500A) Processing sheet with id= A, 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= B, first strand: chain 'AS' and resid 222 through 224 Processing sheet with id= C, first strand: chain 'AS' and resid 300 through 305 removed outlier: 6.014A pdb=" N LYSAS 272 " --> pdb=" O PROAS 252 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'AT' and resid 230 through 232 removed outlier: 6.848A pdb=" N LEUAT 291 " --> pdb=" O PHEAT 299 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VALAT 301 " --> pdb=" O ARGAT 289 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARGAT 289 " --> pdb=" O VALAT 301 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILEAT 303 " --> pdb=" O ALAAT 287 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALAAT 287 " --> pdb=" O ILEAT 303 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEUAT 305 " --> pdb=" O ASNAT 285 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASNAT 285 " --> pdb=" O LEUAT 305 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N METAT 284 " --> pdb=" O VALAT 273 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYSAT 272 " --> pdb=" O PROAT 252 " (cutoff:3.500A) Processing sheet with id= E, 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= F, first strand: chain 'BO' and resid 230 through 232 removed outlier: 6.774A pdb=" N LEUBO 291 " --> pdb=" O PHEBO 299 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VALBO 301 " --> pdb=" O ARGBO 289 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARGBO 289 " --> pdb=" O VALBO 301 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILEBO 303 " --> pdb=" O ALABO 287 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALABO 287 " --> pdb=" O ILEBO 303 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEUBO 305 " --> pdb=" O ASNBO 285 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASNBO 285 " --> pdb=" O LEUBO 305 " (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= G, first strand: chain 'BP' and resid 222 through 224 Processing sheet with id= H, first strand: chain 'BP' and resid 300 through 305 removed outlier: 5.598A pdb=" N LYSBP 272 " --> pdb=" O PROBP 252 " (cutoff:3.500A) 2556 hydrogen bonds defined for protein. 7512 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: 13.97 Time building geometry restraints manager: 20.19 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: 97.70 - 106.43: 1010 106.43 - 115.16: 26036 115.16 - 123.90: 30684 123.90 - 132.63: 1310 132.63 - 141.36: 50 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: 801 2.62 - 3.19: 44135 3.19 - 3.76: 74790 3.76 - 4.33: 99882 4.33 - 4.90: 161867 Nonbonded interactions: 381475 Sorted by model distance: nonbonded pdb=" O GLYAF 111 " pdb=" OG1 THRAF 115 " model vdw 2.056 2.440 nonbonded pdb=" O LYSBM 806 " pdb=" OH TYRBM 873 " model vdw 2.069 2.440 nonbonded pdb=" O ARGAE 16 " pdb=" OH TYRAF 94 " model vdw 2.070 2.440 nonbonded pdb=" OD2 ASPAH 100 " pdb=" OG1 THRAH 102 " model vdw 2.074 2.440 nonbonded pdb=" OD1 ASNAE 71 " pdb=" OG1 THRAE 121 " model vdw 2.080 2.440 ... (remaining 381470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 2.710 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: 0.050 Extract box with map and model: 12.400 Check model and map are aligned: 0.660 Set scattering table: 0.420 Process input model: 113.270 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.720 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: 0.010 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.510 ------------------------------------------------------------------------------- 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= 0.287 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 fitting. rotamer outliers: 2 poor density : 758 time to evaluate : 5.127 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: 1.6646 time to fit residues: 1522.9769 Evaluate side-chains 505 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 502 time to evaluate : 4.714 ------------------------------------------------------------------------------- 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: 3.9990 chunk 409 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 276 optimal weight: 0.1980 chunk 218 optimal weight: 5.9990 chunk 423 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 315 optimal weight: 6.9990 chunk 490 optimal weight: 30.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 2 GLN AD 128 GLN AE 53 GLN AF 71 ASN AF 128 GLN ** AH 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** AS 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 71 ASN ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 131 GLN BF 71 ASN ** BG 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 865 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43584 Z= 0.218 Angle : 0.670 12.019 59090 Z= 0.326 Chirality : 0.041 0.319 6668 Planarity : 0.004 0.055 7602 Dihedral : 8.479 87.036 7174 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.76 % Favored : 97.15 % Rotamer: Outliers : 2.04 % Allowed : 12.84 % Favored : 85.12 % 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: 1.19 (0.12), residues: 5398 helix: 1.51 (0.08), residues: 3818 sheet: -0.62 (0.39), residues: 166 loop : -0.95 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPAS 288 HIS 0.002 0.001 HISBM 807 PHE 0.022 0.002 PHEAU 203 TYR 0.025 0.001 TYRAJ 88 ARG 0.010 0.000 ARGAT 242 *********************** 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 701 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 611 time to evaluate : 5.019 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 6 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8385 (mmmm) REVERT: AA 77 MET cc_start: 0.7763 (mmm) cc_final: 0.7308 (mpp) REVERT: AB 1 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6594 (ttt) REVERT: AC 27 LYS cc_start: 0.9283 (tppt) cc_final: 0.8961 (tppt) REVERT: AC 107 ILE cc_start: 0.9276 (mm) cc_final: 0.9053 (mm) REVERT: AD 28 LYS cc_start: 0.9060 (mtmm) cc_final: 0.8739 (mtmp) REVERT: AD 35 GLU cc_start: 0.8508 (tp30) cc_final: 0.8302 (mm-30) REVERT: AD 54 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: AD 114 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8073 (pp20) REVERT: AF 135 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: AH 6 LYS cc_start: 0.8671 (tmtt) cc_final: 0.8340 (tmmt) REVERT: AJ 60 GLN cc_start: 0.7881 (mt0) cc_final: 0.7678 (tm-30) REVERT: AK 17 LYS cc_start: 0.8477 (mptt) cc_final: 0.8201 (mmtt) REVERT: AK 28 LYS cc_start: 0.8867 (mtmm) cc_final: 0.8630 (mtmt) REVERT: AO 26 TYR cc_start: 0.8343 (t80) cc_final: 0.8115 (t80) REVERT: AQ 817 LYS cc_start: 0.8859 (tmtt) cc_final: 0.8642 (tptp) REVERT: AS 201 TYR cc_start: 0.7951 (t80) cc_final: 0.7738 (t80) REVERT: AT 299 PHE cc_start: 0.7831 (t80) cc_final: 0.7583 (t80) REVERT: AW 6 LYS cc_start: 0.8439 (tmmt) cc_final: 0.8239 (tmmt) REVERT: AW 60 GLN cc_start: 0.8258 (mp10) cc_final: 0.7840 (mp10) REVERT: AW 77 MET cc_start: 0.8875 (mmt) cc_final: 0.8462 (mmp) REVERT: AX 147 LYS cc_start: 0.9191 (ttmm) cc_final: 0.8950 (ttpp) REVERT: AY 6 LYS cc_start: 0.9037 (tppp) cc_final: 0.8438 (tppp) REVERT: AY 10 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8677 (m110) REVERT: AY 73 TYR cc_start: 0.8040 (t80) cc_final: 0.7542 (t80) REVERT: AZ 53 LYS cc_start: 0.9005 (tttt) cc_final: 0.8781 (tttm) REVERT: BD 6 LYS cc_start: 0.7822 (ptmt) cc_final: 0.7500 (ptpp) REVERT: BD 85 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6798 (mmm) REVERT: BD 160 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7551 (tmm) REVERT: BE 43 VAL cc_start: 0.9158 (t) cc_final: 0.8937 (p) REVERT: BE 128 GLN cc_start: 0.8615 (tt0) cc_final: 0.8310 (tm-30) REVERT: BF 56 ASP cc_start: 0.8573 (t0) cc_final: 0.7670 (t0) REVERT: BF 60 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: BH 154 ASP cc_start: 0.8737 (m-30) cc_final: 0.8426 (m-30) REVERT: BO 243 GLU cc_start: 0.7810 (pt0) cc_final: 0.7284 (tm-30) REVERT: BO 268 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8402 (tppt) REVERT: BO 286 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7352 (tt) REVERT: BO 288 TRP cc_start: 0.7130 (m-90) cc_final: 0.6435 (m-90) REVERT: BO 293 ASN cc_start: 0.8740 (t0) cc_final: 0.8462 (t0) REVERT: BO 300 PHE cc_start: 0.8882 (t80) cc_final: 0.8645 (t80) REVERT: BR 241 ASN cc_start: 0.8668 (p0) cc_final: 0.8236 (p0) outliers start: 90 outliers final: 27 residues processed: 651 average time/residue: 1.6267 time to fit residues: 1287.6534 Evaluate side-chains 541 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 505 time to evaluate : 4.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AB residue 1 MET 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 AD residue 114 GLU Chi-restraints excluded: chain AD residue 161 SER Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AI residue 97 LEU Chi-restraints excluded: chain AJ residue 8 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 AS residue 21 VAL Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AX residue 54 GLU Chi-restraints excluded: chain AY residue 10 ASN Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 85 MET Chi-restraints excluded: chain BD residue 102 THR Chi-restraints excluded: chain BD residue 133 MET Chi-restraints excluded: chain BD residue 160 MET Chi-restraints excluded: chain BF residue 60 GLN Chi-restraints excluded: chain BG residue 106 GLU Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BH residue 144 ASP 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 314 ASN Chi-restraints excluded: chain BR residue 239 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 408 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 135 optimal weight: 0.0030 chunk 491 optimal weight: 10.0000 chunk 530 optimal weight: 0.0000 chunk 437 optimal weight: 3.9990 chunk 487 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 394 optimal weight: 2.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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 71 ASN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 128 GLN ** 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** ** AS 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 200 ASN ** 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 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** BP 143 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: 0.8140 moved from start: 0.1722 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= 0.204 Angle : 0.633 12.234 59090 Z= 0.308 Chirality : 0.039 0.256 6668 Planarity : 0.004 0.051 7602 Dihedral : 8.288 88.441 7170 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.96 % Rotamer: Outliers : 2.72 % Allowed : 15.74 % Favored : 81.53 % 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: 1.20 (0.12), residues: 5398 helix: 1.53 (0.08), residues: 3825 sheet: -0.84 (0.37), residues: 182 loop : -0.95 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAT 288 HIS 0.002 0.001 HISBM 807 PHE 0.028 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 689 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 569 time to evaluate : 5.758 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: AA 77 MET cc_start: 0.7469 (mmm) cc_final: 0.7089 (mpp) REVERT: AC 27 LYS cc_start: 0.9297 (tppt) cc_final: 0.9052 (tppt) REVERT: AC 107 ILE cc_start: 0.9271 (mm) cc_final: 0.9057 (mm) REVERT: AD 28 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8778 (mtmp) REVERT: AD 35 GLU cc_start: 0.8479 (tp30) cc_final: 0.8224 (mm-30) REVERT: AF 135 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: AH 6 LYS cc_start: 0.8656 (tmtt) cc_final: 0.8312 (tmmt) REVERT: AK 17 LYS cc_start: 0.8528 (mptt) cc_final: 0.8254 (mmtt) REVERT: AK 28 LYS cc_start: 0.8894 (mtmm) cc_final: 0.8611 (mtmp) REVERT: AQ 817 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8655 (tptp) REVERT: AT 264 PHE cc_start: 0.5802 (m-80) cc_final: 0.5512 (m-80) REVERT: AT 284 MET cc_start: 0.6594 (mmm) cc_final: 0.6390 (mmm) REVERT: AW 60 GLN cc_start: 0.8310 (mp10) cc_final: 0.7898 (mp10) REVERT: AX 54 GLU cc_start: 0.8012 (mp0) cc_final: 0.7713 (mp0) REVERT: AX 73 TYR cc_start: 0.7034 (t80) cc_final: 0.6829 (t80) REVERT: AX 147 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8982 (ttpp) REVERT: AY 73 TYR cc_start: 0.7980 (t80) cc_final: 0.7505 (t80) REVERT: AZ 28 LYS cc_start: 0.8999 (mtmt) cc_final: 0.8755 (mtmt) REVERT: AZ 53 LYS cc_start: 0.9000 (tttt) cc_final: 0.8765 (tttm) REVERT: BD 160 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7579 (tmm) REVERT: BF 56 ASP cc_start: 0.8614 (t0) cc_final: 0.8062 (t0) REVERT: BF 60 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: BH 154 ASP cc_start: 0.8731 (m-30) cc_final: 0.8421 (m-30) REVERT: BO 243 GLU cc_start: 0.7833 (pt0) cc_final: 0.7248 (tm-30) REVERT: BO 286 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7362 (tt) REVERT: BO 288 TRP cc_start: 0.7246 (m-90) cc_final: 0.6525 (m-90) REVERT: BO 293 ASN cc_start: 0.8542 (t0) cc_final: 0.8289 (t0) REVERT: BO 297 LYS cc_start: 0.9002 (mtpp) cc_final: 0.8756 (mtpp) REVERT: BR 208 LYS cc_start: 0.8331 (mptt) cc_final: 0.8111 (pptt) REVERT: BR 241 ASN cc_start: 0.8616 (p0) cc_final: 0.8195 (p0) outliers start: 120 outliers final: 40 residues processed: 633 average time/residue: 1.6173 time to fit residues: 1243.6465 Evaluate side-chains 537 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 493 time to evaluate : 4.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AB residue 72 MET Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 161 SER Chi-restraints excluded: chain AD residue 54 GLU Chi-restraints excluded: chain AF residue 126 THR Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AJ residue 8 ILE Chi-restraints excluded: chain AJ residue 53 GLN Chi-restraints excluded: chain AK residue 115 THR 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 726 LEU Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 286 ILE Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AY residue 50 ILE Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AY residue 102 THR Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BD residue 102 THR Chi-restraints excluded: chain BD residue 160 MET Chi-restraints excluded: chain BF residue 60 GLN Chi-restraints excluded: chain BG residue 106 GLU 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 286 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 BP residue 314 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: 0.7980 chunk 254 optimal weight: 40.0000 chunk 54 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 493 optimal weight: 8.9990 chunk 521 optimal weight: 0.9990 chunk 257 optimal weight: 30.0000 chunk 467 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 71 ASN ** 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** ** AS 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 281 ASN ** 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** ** BB 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** BI 71 ASN BI 128 GLN ** BO 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 217 ASN ** 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: 0.8182 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 43584 Z= 0.275 Angle : 0.655 11.934 59090 Z= 0.320 Chirality : 0.040 0.278 6668 Planarity : 0.004 0.056 7602 Dihedral : 8.126 92.337 7168 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 3.63 % Allowed : 17.45 % Favored : 78.92 % 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: 1.23 (0.12), residues: 5398 helix: 1.55 (0.08), residues: 3813 sheet: -0.82 (0.37), residues: 186 loop : -0.92 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPAT 288 HIS 0.002 0.001 HISBM 807 PHE 0.021 0.001 PHEAU 203 TYR 0.025 0.002 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 694 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 534 time to evaluate : 5.353 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: AA 6 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8311 (mmmm) REVERT: AA 77 MET cc_start: 0.7471 (mmm) cc_final: 0.7098 (mpp) REVERT: AB 1 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6787 (ttt) REVERT: AC 56 ASP cc_start: 0.8661 (m-30) cc_final: 0.8459 (m-30) REVERT: AC 107 ILE cc_start: 0.9299 (mm) cc_final: 0.9078 (mm) REVERT: AD 149 MET cc_start: 0.8938 (mmm) cc_final: 0.8568 (tpt) REVERT: AE 160 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8403 (ttm) REVERT: AF 135 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: AH 6 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8343 (tmmt) REVERT: AH 87 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.6812 (m-10) REVERT: AK 17 LYS cc_start: 0.8537 (mptt) cc_final: 0.8244 (mmtt) REVERT: AK 28 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8615 (mtmp) REVERT: AL 6 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8178 (mttp) REVERT: AM 77 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8190 (mtm-85) REVERT: AQ 817 LYS cc_start: 0.8885 (tmtt) cc_final: 0.8643 (tptp) REVERT: AS 201 TYR cc_start: 0.8075 (t80) cc_final: 0.7823 (t80) REVERT: AT 235 GLU cc_start: 0.6942 (tp30) cc_final: 0.6713 (tt0) REVERT: AT 281 ASN cc_start: 0.7562 (m-40) cc_final: 0.7348 (t0) REVERT: AT 284 MET cc_start: 0.6671 (mmm) cc_final: 0.6459 (mmm) REVERT: AT 289 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7428 (ttt180) REVERT: AW 60 GLN cc_start: 0.8363 (mp10) cc_final: 0.7935 (mp10) REVERT: AX 54 GLU cc_start: 0.8057 (mp0) cc_final: 0.7641 (mp0) REVERT: AX 147 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8998 (ttpp) REVERT: AY 88 TYR cc_start: 0.7940 (m-80) cc_final: 0.7732 (m-80) REVERT: BD 6 LYS cc_start: 0.8008 (ptmt) cc_final: 0.7652 (ptpp) REVERT: BD 160 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7619 (tmm) REVERT: BF 56 ASP cc_start: 0.8616 (t0) cc_final: 0.7891 (t0) REVERT: BF 60 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: BG 1 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7511 (ptm) REVERT: BH 154 ASP cc_start: 0.8753 (m-30) cc_final: 0.8435 (m-30) REVERT: BI 54 GLU cc_start: 0.7860 (pm20) cc_final: 0.7260 (pm20) REVERT: BO 242 ARG cc_start: 0.8977 (ptp-110) cc_final: 0.8736 (ptp90) REVERT: BO 268 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7953 (tppt) REVERT: BO 293 ASN cc_start: 0.8549 (t0) cc_final: 0.8285 (t0) REVERT: BO 300 PHE cc_start: 0.9119 (t80) cc_final: 0.8912 (t80) REVERT: BR 208 LYS cc_start: 0.8319 (mptt) cc_final: 0.8037 (pptt) REVERT: BR 241 ASN cc_start: 0.8707 (p0) cc_final: 0.8301 (p0) outliers start: 160 outliers final: 54 residues processed: 626 average time/residue: 1.6467 time to fit residues: 1259.4425 Evaluate side-chains 539 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 476 time to evaluate : 5.179 ------------------------------------------------------------------------------- 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 108 VAL Chi-restraints excluded: chain AC residue 17 TYR Chi-restraints excluded: chain AC residue 161 SER Chi-restraints excluded: chain AD residue 54 GLU Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 126 THR Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AH 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 AJ residue 78 THR Chi-restraints excluded: chain AJ residue 144 ASP Chi-restraints excluded: chain AM residue 77 ARG 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 805 THR Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 286 ILE Chi-restraints excluded: chain AT residue 289 ARG Chi-restraints excluded: chain AU residue 214 ASN Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 54 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 102 THR Chi-restraints excluded: chain BD residue 160 MET Chi-restraints excluded: chain BE residue 14 VAL Chi-restraints excluded: chain BF residue 60 GLN Chi-restraints excluded: chain BG residue 1 MET Chi-restraints excluded: chain BG residue 106 GLU 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 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 BM residue 710 SER 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 BP residue 314 ASN Chi-restraints excluded: chain BR residue 221 MET Chi-restraints excluded: chain BR residue 239 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 0.6980 chunk 296 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 445 optimal weight: 0.9980 chunk 360 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 468 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 128 GLN 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 274 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** ** AZ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 10 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** ** BI 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 204 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43584 Z= 0.289 Angle : 0.669 12.190 59090 Z= 0.327 Chirality : 0.041 0.249 6668 Planarity : 0.004 0.053 7602 Dihedral : 8.045 91.369 7168 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 3.56 % Allowed : 18.76 % Favored : 77.68 % 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: 1.21 (0.12), residues: 5398 helix: 1.52 (0.08), residues: 3813 sheet: -0.65 (0.38), residues: 190 loop : -0.92 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAT 288 HIS 0.002 0.001 HISBM 807 PHE 0.019 0.001 PHEAU 203 TYR 0.027 0.002 TYRAE 73 ARG 0.009 0.000 ARGAB 39 *********************** 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 676 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 519 time to evaluate : 5.044 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: 0.7486 (mmm) cc_final: 0.7135 (mpp) REVERT: AB 1 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6940 (ttt) REVERT: AB 53 LYS cc_start: 0.9251 (tttt) cc_final: 0.9050 (tttp) REVERT: AC 107 ILE cc_start: 0.9304 (mm) cc_final: 0.9078 (mm) REVERT: AD 149 MET cc_start: 0.8922 (mmm) cc_final: 0.8634 (tpt) REVERT: AE 115 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8387 (ttt) REVERT: AF 135 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: AH 6 LYS cc_start: 0.8731 (tmtt) cc_final: 0.8305 (tmmt) REVERT: AH 87 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6870 (m-10) REVERT: AH 160 MET cc_start: 0.8342 (ppp) cc_final: 0.8047 (ptt) REVERT: AJ 8 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9287 (mp) REVERT: AK 17 LYS cc_start: 0.8547 (mptt) cc_final: 0.8236 (mmtt) REVERT: AK 28 LYS cc_start: 0.8942 (mtmm) cc_final: 0.8624 (mtmp) REVERT: AM 77 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8234 (mtm-85) REVERT: AS 61 MET cc_start: 0.7120 (tpt) cc_final: 0.6879 (tpt) REVERT: AS 205 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8763 (pp) REVERT: AS 250 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8212 (mp) REVERT: AT 235 GLU cc_start: 0.7168 (tp30) cc_final: 0.6931 (tt0) REVERT: AT 284 MET cc_start: 0.6699 (mmm) cc_final: 0.6444 (mmm) REVERT: AT 289 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7394 (ttt180) REVERT: AW 60 GLN cc_start: 0.8400 (mp10) cc_final: 0.8024 (mp10) REVERT: AX 54 GLU cc_start: 0.8076 (mp0) cc_final: 0.7653 (mp0) REVERT: AX 147 LYS cc_start: 0.9268 (ttmm) cc_final: 0.9034 (ttpp) REVERT: AY 77 MET cc_start: 0.6917 (mmp) cc_final: 0.6549 (mmp) REVERT: AY 100 ASP cc_start: 0.7997 (p0) cc_final: 0.7719 (p0) REVERT: BD 6 LYS cc_start: 0.8032 (ptmt) cc_final: 0.7648 (ptpp) REVERT: BD 160 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7648 (tmm) REVERT: BE 43 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8996 (p) REVERT: BG 1 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7530 (ptm) REVERT: BG 15 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: BH 154 ASP cc_start: 0.8741 (m-30) cc_final: 0.8429 (m-30) REVERT: BI 15 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8309 (mp10) REVERT: BI 54 GLU cc_start: 0.7871 (pm20) cc_final: 0.7332 (pm20) REVERT: BO 215 GLU cc_start: 0.8656 (mp0) cc_final: 0.8374 (mp0) REVERT: BO 242 ARG cc_start: 0.9023 (ptp-110) cc_final: 0.8778 (ptp90) REVERT: BO 268 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7679 (tppt) REVERT: BO 293 ASN cc_start: 0.8510 (t0) cc_final: 0.8263 (t0) REVERT: BO 300 PHE cc_start: 0.9116 (t80) cc_final: 0.8907 (t80) REVERT: BR 241 ASN cc_start: 0.8779 (p0) cc_final: 0.8379 (p0) outliers start: 157 outliers final: 68 residues processed: 620 average time/residue: 1.5828 time to fit residues: 1197.1594 Evaluate side-chains 555 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 473 time to evaluate : 5.107 ------------------------------------------------------------------------------- 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 108 VAL 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 161 SER Chi-restraints excluded: chain AD residue 54 GLU Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 126 THR Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AF residue 141 VAL Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AH residue 87 TYR Chi-restraints excluded: chain AH residue 110 VAL Chi-restraints excluded: chain AI residue 72 MET Chi-restraints excluded: chain AI residue 87 TYR Chi-restraints excluded: chain AI residue 126 THR Chi-restraints excluded: chain AJ residue 8 ILE Chi-restraints excluded: chain AJ residue 78 THR Chi-restraints excluded: chain AJ residue 144 ASP Chi-restraints excluded: chain AM residue 77 ARG Chi-restraints excluded: chain AM residue 135 GLU Chi-restraints excluded: chain AM residue 137 THR Chi-restraints excluded: chain AM 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 750 ASP Chi-restraints excluded: chain AQ residue 751 LEU Chi-restraints excluded: chain AQ residue 805 THR Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 74 MET Chi-restraints excluded: chain AS residue 205 LEU Chi-restraints excluded: chain AS residue 250 LEU Chi-restraints excluded: chain AT residue 286 ILE Chi-restraints excluded: chain AT residue 289 ARG Chi-restraints excluded: chain AU residue 235 VAL Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AW residue 4 VAL Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 50 ILE Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 137 THR 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 102 THR Chi-restraints excluded: chain BD residue 160 MET Chi-restraints excluded: chain BE residue 14 VAL Chi-restraints excluded: chain BE residue 43 VAL Chi-restraints excluded: chain BE residue 44 ILE Chi-restraints excluded: chain BG residue 1 MET Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 106 GLU Chi-restraints excluded: chain BG residue 161 SER Chi-restraints excluded: chain BH residue 30 VAL 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 15 GLN 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 BM residue 710 SER 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 BP residue 314 ASN Chi-restraints excluded: chain BQ residue 236 SER Chi-restraints excluded: chain BQ residue 245 SER Chi-restraints excluded: chain BR residue 204 ILE Chi-restraints excluded: chain BR residue 221 MET Chi-restraints excluded: chain BR residue 239 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 0.9990 chunk 470 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 306 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 522 optimal weight: 9.9990 chunk 433 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 43 optimal weight: 0.0980 chunk 172 optimal weight: 1.9990 chunk 274 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 128 GLN ** AF 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 53 GLN ** AK 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 285 ASN ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 10 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** ** BI 15 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 43584 Z= 0.194 Angle : 0.652 12.136 59090 Z= 0.317 Chirality : 0.039 0.233 6668 Planarity : 0.004 0.071 7602 Dihedral : 7.939 87.678 7168 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.96 % Rotamer: Outliers : 2.95 % Allowed : 20.51 % Favored : 76.54 % 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: 1.34 (0.12), residues: 5398 helix: 1.58 (0.08), residues: 3795 sheet: -0.21 (0.40), residues: 174 loop : -0.78 (0.17), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPBO 288 HIS 0.001 0.001 HISBM 807 PHE 0.018 0.001 PHEAU 203 TYR 0.027 0.001 TYRAE 73 ARG 0.014 0.000 ARGBK 59 *********************** 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 679 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 549 time to evaluate : 5.424 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: AA 6 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8475 (mmmm) REVERT: AA 77 MET cc_start: 0.7405 (mmm) cc_final: 0.7048 (mpp) REVERT: AB 1 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6877 (ttt) REVERT: AC 107 ILE cc_start: 0.9304 (mm) cc_final: 0.9084 (mm) REVERT: AC 123 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.9004 (pp) REVERT: AC 159 LYS cc_start: 0.9299 (tptm) cc_final: 0.9029 (tptm) REVERT: AD 149 MET cc_start: 0.8867 (mmm) cc_final: 0.8655 (tpt) REVERT: AE 115 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8354 (ttt) REVERT: AE 160 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8428 (ttm) REVERT: AF 135 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: AH 6 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8329 (tmmt) REVERT: AH 60 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: AH 141 MET cc_start: 0.7857 (ptp) cc_final: 0.7568 (ppp) REVERT: AH 160 MET cc_start: 0.8209 (ppp) cc_final: 0.7961 (ptt) REVERT: AI 149 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8410 (mmm) REVERT: AK 17 LYS cc_start: 0.8568 (mptt) cc_final: 0.8283 (mmtt) REVERT: AK 28 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8589 (mtmp) REVERT: AL 6 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8383 (mtmp) REVERT: AM 77 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8224 (mtm-85) REVERT: AM 135 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: AS 250 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8146 (mp) REVERT: AT 289 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7413 (ttt180) REVERT: AW 60 GLN cc_start: 0.8391 (mp10) cc_final: 0.8049 (mp10) REVERT: AX 28 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8147 (mmmt) REVERT: AX 54 GLU cc_start: 0.8059 (mp0) cc_final: 0.7717 (mp0) REVERT: AX 147 LYS cc_start: 0.9246 (ttmm) cc_final: 0.9028 (ttpp) REVERT: AY 88 TYR cc_start: 0.7911 (m-80) cc_final: 0.7710 (m-80) REVERT: AY 100 ASP cc_start: 0.7833 (p0) cc_final: 0.7536 (p0) REVERT: BD 6 LYS cc_start: 0.7975 (ptmt) cc_final: 0.7622 (ptpp) REVERT: BE 43 VAL cc_start: 0.9133 (t) cc_final: 0.8901 (p) REVERT: BG 1 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7470 (ptm) REVERT: BH 24 ASP cc_start: 0.8592 (m-30) cc_final: 0.8390 (p0) REVERT: BH 154 ASP cc_start: 0.8732 (m-30) cc_final: 0.8411 (m-30) REVERT: BI 15 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: BI 54 GLU cc_start: 0.7821 (pm20) cc_final: 0.7346 (pm20) REVERT: BO 215 GLU cc_start: 0.8653 (mp0) cc_final: 0.8413 (mp0) REVERT: BO 268 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7828 (tppt) REVERT: BO 286 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8397 (tp) REVERT: BO 293 ASN cc_start: 0.8529 (t0) cc_final: 0.8297 (t0) REVERT: BR 241 ASN cc_start: 0.8679 (p0) cc_final: 0.8290 (p0) outliers start: 130 outliers final: 56 residues processed: 624 average time/residue: 1.6175 time to fit residues: 1230.9628 Evaluate side-chains 561 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 491 time to evaluate : 4.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL 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 123 ILE Chi-restraints excluded: chain AD residue 54 GLU Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 126 THR Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AF residue 141 VAL Chi-restraints excluded: chain AH residue 3 ILE Chi-restraints excluded: chain AH residue 60 GLN Chi-restraints excluded: chain AI residue 126 THR Chi-restraints excluded: chain AI residue 149 MET Chi-restraints excluded: chain AJ residue 8 ILE Chi-restraints excluded: chain AJ residue 53 GLN Chi-restraints excluded: chain AJ residue 144 ASP Chi-restraints excluded: chain AM residue 77 ARG Chi-restraints excluded: chain AM residue 135 GLU Chi-restraints excluded: chain AM residue 137 THR Chi-restraints excluded: chain AM 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 751 LEU Chi-restraints excluded: chain AQ residue 805 THR Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 250 LEU Chi-restraints excluded: chain AS residue 269 VAL Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 286 ILE Chi-restraints excluded: chain AT residue 289 ARG Chi-restraints excluded: chain AU residue 214 ASN Chi-restraints excluded: chain AU residue 235 VAL Chi-restraints excluded: chain AV residue 240 ILE Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AY residue 50 ILE Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 54 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 102 THR Chi-restraints excluded: chain BG residue 1 MET Chi-restraints excluded: chain BG residue 36 LEU Chi-restraints excluded: chain BG residue 106 GLU 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 15 GLN Chi-restraints excluded: chain BI residue 58 LYS 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 286 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 BP residue 314 ASN Chi-restraints excluded: chain BQ residue 236 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: 9.9990 chunk 58 optimal weight: 1.9990 chunk 297 optimal weight: 6.9990 chunk 381 optimal weight: 5.9990 chunk 295 optimal weight: 0.9990 chunk 439 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 520 optimal weight: 20.0000 chunk 325 optimal weight: 0.9990 chunk 317 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 128 GLN ** AF 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 246 GLN ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 10 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** ** BI 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 204 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43584 Z= 0.227 Angle : 0.675 13.653 59090 Z= 0.326 Chirality : 0.040 0.257 6668 Planarity : 0.004 0.052 7602 Dihedral : 7.935 87.120 7168 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 3.04 % Allowed : 21.46 % Favored : 75.50 % 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: 1.29 (0.12), residues: 5398 helix: 1.56 (0.08), residues: 3786 sheet: -0.04 (0.42), residues: 154 loop : -0.86 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRPBO 288 HIS 0.001 0.001 HISBM 807 PHE 0.026 0.001 PHEAU 203 TYR 0.027 0.001 TYRAE 73 ARG 0.011 0.000 ARGBR 202 *********************** 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 647 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 513 time to evaluate : 5.485 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: AA 77 MET cc_start: 0.7376 (mmm) cc_final: 0.7069 (mpp) REVERT: AA 141 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7218 (pp-130) REVERT: AB 1 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6913 (ttt) REVERT: AB 53 LYS cc_start: 0.9227 (tttt) cc_final: 0.9006 (tttp) REVERT: AC 107 ILE cc_start: 0.9271 (mm) cc_final: 0.9068 (mm) REVERT: AC 123 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.9009 (pp) REVERT: AC 159 LYS cc_start: 0.9309 (tptm) cc_final: 0.9043 (tptm) REVERT: AD 149 MET cc_start: 0.8785 (mmm) cc_final: 0.8580 (tpt) REVERT: AE 115 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8250 (ttt) REVERT: AE 160 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8451 (ttm) REVERT: AF 135 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: AH 6 LYS cc_start: 0.8744 (tmtt) cc_final: 0.8328 (tmmt) REVERT: AH 60 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: AH 87 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: AH 141 MET cc_start: 0.7798 (ptp) cc_final: 0.7536 (ppp) REVERT: AI 149 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8447 (mmm) REVERT: AK 17 LYS cc_start: 0.8576 (mptt) cc_final: 0.8285 (mmtt) REVERT: AK 28 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8598 (mtmp) REVERT: AM 77 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8222 (mtm-85) REVERT: AM 135 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: AT 289 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7434 (ttt180) REVERT: AW 60 GLN cc_start: 0.8409 (mp10) cc_final: 0.8068 (mp10) REVERT: AX 54 GLU cc_start: 0.8068 (mp0) cc_final: 0.7710 (mp0) REVERT: AX 147 LYS cc_start: 0.9255 (ttmm) cc_final: 0.9040 (ttpp) REVERT: AY 77 MET cc_start: 0.6807 (mmp) cc_final: 0.6505 (mmp) REVERT: AY 100 ASP cc_start: 0.7843 (p0) cc_final: 0.7563 (p0) REVERT: BD 6 LYS cc_start: 0.7968 (ptmt) cc_final: 0.7561 (ptpp) REVERT: BE 43 VAL cc_start: 0.9176 (t) cc_final: 0.8969 (p) REVERT: BG 15 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: BH 154 ASP cc_start: 0.8741 (m-30) cc_final: 0.8431 (m-30) REVERT: BI 15 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: BI 54 GLU cc_start: 0.7827 (pm20) cc_final: 0.7349 (pm20) REVERT: BO 293 ASN cc_start: 0.8542 (t0) cc_final: 0.8284 (t0) REVERT: BR 241 ASN cc_start: 0.8650 (p0) cc_final: 0.8284 (p0) outliers start: 134 outliers final: 63 residues processed: 597 average time/residue: 1.6375 time to fit residues: 1188.5102 Evaluate side-chains 558 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 481 time to evaluate : 5.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AA residue 141 MET Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 108 VAL Chi-restraints excluded: chain AB residue 133 ILE 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 54 GLU Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 126 THR Chi-restraints excluded: chain AF residue 135 GLU Chi-restraints excluded: chain AF residue 141 VAL 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 72 MET Chi-restraints excluded: chain AI residue 97 LEU Chi-restraints excluded: chain AI residue 126 THR Chi-restraints excluded: chain AI residue 149 MET Chi-restraints excluded: chain AJ residue 8 ILE Chi-restraints excluded: chain AJ residue 53 GLN Chi-restraints excluded: chain AJ residue 144 ASP Chi-restraints excluded: chain AM residue 77 ARG Chi-restraints excluded: chain AM residue 135 GLU Chi-restraints excluded: chain AM residue 137 THR Chi-restraints excluded: chain AM 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 751 LEU Chi-restraints excluded: chain AQ residue 805 THR Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 269 VAL Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 286 ILE Chi-restraints excluded: chain AT residue 289 ARG 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 108 VAL Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 50 ILE Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 137 THR Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 106 GLU 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 BH residue 133 MET Chi-restraints excluded: chain BH residue 141 MET Chi-restraints excluded: chain BI residue 15 GLN Chi-restraints excluded: chain BI residue 58 LYS 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 281 ASN 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 BP residue 83 MET Chi-restraints excluded: chain BP residue 314 ASN Chi-restraints excluded: chain BQ residue 236 SER Chi-restraints excluded: chain BQ residue 245 SER Chi-restraints excluded: chain BR residue 239 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 330 optimal weight: 3.9990 chunk 354 optimal weight: 6.9990 chunk 257 optimal weight: 40.0000 chunk 48 optimal weight: 0.4980 chunk 409 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** AF 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 274 GLN AT 281 ASN ** AX 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 10 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** ** BI 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8142 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43584 Z= 0.195 Angle : 0.678 13.561 59090 Z= 0.327 Chirality : 0.039 0.218 6668 Planarity : 0.004 0.081 7602 Dihedral : 7.929 88.221 7168 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 2.59 % Allowed : 22.01 % Favored : 75.41 % 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: 1.29 (0.12), residues: 5398 helix: 1.53 (0.08), residues: 3800 sheet: 0.01 (0.43), residues: 154 loop : -0.81 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPBO 288 HIS 0.001 0.001 HISBM 807 PHE 0.025 0.001 PHEAU 203 TYR 0.028 0.001 TYRAE 73 ARG 0.018 0.000 ARGBK 59 *********************** 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 634 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 520 time to evaluate : 4.792 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: AA 77 MET cc_start: 0.7296 (mmm) cc_final: 0.7011 (mpp) REVERT: AA 141 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7231 (pp-130) REVERT: AB 1 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6858 (ttt) REVERT: AC 123 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9032 (pp) REVERT: AC 159 LYS cc_start: 0.9306 (tptm) cc_final: 0.9047 (tptm) REVERT: AD 149 MET cc_start: 0.8833 (mmm) cc_final: 0.8619 (tpt) REVERT: AE 115 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8318 (ttt) REVERT: AE 160 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8425 (ttm) REVERT: AF 135 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: AH 6 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8311 (tmmt) REVERT: AH 60 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: AI 152 TYR cc_start: 0.7531 (m-10) cc_final: 0.7202 (m-80) REVERT: AJ 8 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.9270 (mp) REVERT: AK 17 LYS cc_start: 0.8540 (mptt) cc_final: 0.8270 (mmtt) REVERT: AK 28 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8551 (mtmm) REVERT: AK 148 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7963 (mt-10) REVERT: AM 77 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8144 (mtm-85) REVERT: AT 289 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7503 (ttt180) REVERT: AT 297 LYS cc_start: 0.8423 (mmmm) cc_final: 0.8187 (mmmm) REVERT: AU 207 GLU cc_start: 0.7696 (pp20) cc_final: 0.7445 (pm20) REVERT: AW 60 GLN cc_start: 0.8377 (mp10) cc_final: 0.8027 (mp10) REVERT: AX 54 GLU cc_start: 0.8074 (mp0) cc_final: 0.7754 (mp0) REVERT: AX 147 LYS cc_start: 0.9246 (ttmm) cc_final: 0.9038 (ttpp) REVERT: AY 77 MET cc_start: 0.6860 (mmp) cc_final: 0.6578 (mmp) REVERT: AY 100 ASP cc_start: 0.7766 (p0) cc_final: 0.7472 (p0) REVERT: AZ 97 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8752 (tt) REVERT: AZ 149 MET cc_start: 0.9253 (mmm) cc_final: 0.8973 (tpt) REVERT: BD 6 LYS cc_start: 0.7893 (ptmt) cc_final: 0.7516 (ptpp) REVERT: BE 24 MET cc_start: 0.7613 (mmm) cc_final: 0.7240 (mmm) REVERT: BG 15 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: BH 24 ASP cc_start: 0.8594 (m-30) cc_final: 0.8386 (p0) REVERT: BH 154 ASP cc_start: 0.8733 (m-30) cc_final: 0.8418 (m-30) REVERT: BI 54 GLU cc_start: 0.7769 (pm20) cc_final: 0.7416 (pm20) REVERT: BO 242 ARG cc_start: 0.9019 (ptp-110) cc_final: 0.8780 (ptp90) REVERT: BO 293 ASN cc_start: 0.8548 (t0) cc_final: 0.8290 (t0) REVERT: BR 241 ASN cc_start: 0.8524 (p0) cc_final: 0.8178 (p0) outliers start: 114 outliers final: 55 residues processed: 589 average time/residue: 1.6407 time to fit residues: 1176.8961 Evaluate side-chains 550 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 483 time to evaluate : 5.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AA residue 141 MET Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 104 LEU Chi-restraints excluded: chain AB residue 108 VAL 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 54 GLU Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 126 THR 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 AJ residue 144 ASP Chi-restraints excluded: chain AK residue 36 LEU Chi-restraints excluded: chain AM residue 77 ARG Chi-restraints excluded: chain AM residue 137 THR Chi-restraints excluded: chain AM 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 751 LEU Chi-restraints excluded: chain AQ residue 805 THR Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 269 VAL Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 286 ILE Chi-restraints excluded: chain AT residue 289 ARG 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 47 ASN Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 35 GLU Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 97 LEU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 106 GLU Chi-restraints excluded: chain BH residue 8 ILE Chi-restraints excluded: chain BH residue 30 VAL Chi-restraints excluded: chain BH residue 81 CYS 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 53 VAL Chi-restraints excluded: chain BK residue 66 LEU Chi-restraints excluded: chain BM residue 700 ILE Chi-restraints excluded: chain BO residue 212 THR Chi-restraints excluded: chain BO residue 281 ASN 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 BP residue 314 ASN Chi-restraints excluded: chain BR residue 204 ILE Chi-restraints excluded: chain BR residue 239 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 6.9990 chunk 498 optimal weight: 20.0000 chunk 454 optimal weight: 0.8980 chunk 485 optimal weight: 0.9990 chunk 291 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 380 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 438 optimal weight: 3.9990 chunk 458 optimal weight: 1.9990 chunk 483 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 128 GLN ** AF 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 274 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** ** BB 10 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** ** BI 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43584 Z= 0.237 Angle : 0.705 17.550 59090 Z= 0.341 Chirality : 0.040 0.232 6668 Planarity : 0.004 0.054 7602 Dihedral : 7.954 86.440 7168 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 2.45 % Allowed : 22.46 % Favored : 75.09 % 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: 1.29 (0.12), residues: 5398 helix: 1.56 (0.08), residues: 3790 sheet: -0.31 (0.41), residues: 170 loop : -0.81 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPBO 288 HIS 0.001 0.001 HISAQ 807 PHE 0.024 0.001 PHEAU 203 TYR 0.030 0.001 TYRAE 73 ARG 0.013 0.000 ARGBR 202 *********************** 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 608 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 500 time to evaluate : 5.291 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: AA 77 MET cc_start: 0.7359 (mmm) cc_final: 0.7045 (mpp) REVERT: AA 141 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7293 (pp-130) REVERT: AB 1 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7010 (ttt) REVERT: AC 123 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9031 (pp) REVERT: AE 115 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8338 (ttt) REVERT: AE 160 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8455 (ttm) REVERT: AF 96 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7033 (ttm) REVERT: AF 135 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: AH 6 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8314 (tmmt) REVERT: AH 60 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: AH 87 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.6849 (m-10) REVERT: AI 152 TYR cc_start: 0.7598 (m-10) cc_final: 0.7257 (m-80) REVERT: AJ 53 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: AK 17 LYS cc_start: 0.8571 (mptt) cc_final: 0.8301 (mmtt) REVERT: AK 28 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8542 (mtmm) REVERT: AK 148 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7979 (mt-10) REVERT: AL 6 LYS cc_start: 0.8745 (mtmp) cc_final: 0.8413 (mttp) REVERT: AM 77 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8181 (mtm-85) REVERT: AO 44 MET cc_start: 0.7699 (mtm) cc_final: 0.7380 (mtm) REVERT: AT 289 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7485 (ttt180) REVERT: AW 60 GLN cc_start: 0.8390 (mp10) cc_final: 0.8035 (mp10) REVERT: AX 28 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8126 (mmmt) REVERT: AX 54 GLU cc_start: 0.8075 (mp0) cc_final: 0.7756 (mp0) REVERT: AX 147 LYS cc_start: 0.9258 (ttmm) cc_final: 0.9049 (ttpp) REVERT: AY 77 MET cc_start: 0.6910 (mmp) cc_final: 0.6252 (mmp) REVERT: AY 88 TYR cc_start: 0.7930 (m-80) cc_final: 0.7709 (m-80) REVERT: AY 100 ASP cc_start: 0.7826 (p0) cc_final: 0.7510 (p0) REVERT: AZ 97 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8782 (tt) REVERT: BB 1 MET cc_start: 0.7885 (ttp) cc_final: 0.7594 (tmt) REVERT: BD 6 LYS cc_start: 0.7895 (ptmt) cc_final: 0.7457 (ptpp) REVERT: BD 100 ASP cc_start: 0.6779 (t70) cc_final: 0.6152 (t0) REVERT: BG 15 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: BH 154 ASP cc_start: 0.8740 (m-30) cc_final: 0.8424 (m-30) REVERT: BI 15 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (mp10) REVERT: BI 54 GLU cc_start: 0.7808 (pm20) cc_final: 0.7417 (pm20) REVERT: BO 268 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7893 (tppt) REVERT: BO 293 ASN cc_start: 0.8553 (t0) cc_final: 0.8293 (t0) REVERT: BP 313 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8062 (pp) REVERT: BR 241 ASN cc_start: 0.8538 (p0) cc_final: 0.8208 (p0) outliers start: 108 outliers final: 61 residues processed: 570 average time/residue: 1.7144 time to fit residues: 1196.3184 Evaluate side-chains 550 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 473 time to evaluate : 4.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AA residue 141 MET Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 104 LEU Chi-restraints excluded: chain AB residue 108 VAL Chi-restraints excluded: chain AB residue 133 ILE 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 54 GLU Chi-restraints excluded: chain AD residue 161 SER Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AE residue 133 MET Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 96 MET Chi-restraints excluded: chain AF residue 126 THR 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 53 GLN Chi-restraints excluded: chain AJ residue 144 ASP Chi-restraints excluded: chain AM residue 77 ARG Chi-restraints excluded: chain AM residue 137 THR Chi-restraints excluded: chain AM 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 751 LEU Chi-restraints excluded: chain AQ residue 805 THR Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 269 VAL Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 286 ILE Chi-restraints excluded: chain AT residue 289 ARG 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 47 ASN Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AX residue 156 ILE Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 35 GLU Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 97 LEU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 106 GLU 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 BH residue 141 MET Chi-restraints excluded: chain BI residue 15 GLN Chi-restraints excluded: chain BI residue 58 LYS 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 BM residue 731 ASP Chi-restraints excluded: chain BO residue 281 ASN 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 BP residue 313 LEU Chi-restraints excluded: chain BP residue 314 ASN Chi-restraints excluded: chain BQ residue 236 SER Chi-restraints excluded: chain BQ residue 245 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: 9.9990 chunk 512 optimal weight: 2.9990 chunk 313 optimal weight: 0.4980 chunk 243 optimal weight: 7.9990 chunk 356 optimal weight: 7.9990 chunk 537 optimal weight: 0.6980 chunk 495 optimal weight: 20.0000 chunk 428 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 330 optimal weight: 0.6980 chunk 262 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 128 GLN ** AF 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 35 ASN ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 274 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** ** BB 10 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** ** BI 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 217 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: 0.8149 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43584 Z= 0.217 Angle : 0.717 16.580 59090 Z= 0.348 Chirality : 0.040 0.209 6668 Planarity : 0.004 0.088 7602 Dihedral : 7.971 84.101 7168 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 2.18 % Allowed : 23.14 % 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: 1.25 (0.12), residues: 5398 helix: 1.53 (0.08), residues: 3782 sheet: -0.23 (0.42), residues: 170 loop : -0.84 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPBO 288 HIS 0.001 0.001 HISAQ 807 PHE 0.031 0.001 PHEAU 203 TYR 0.030 0.001 TYRAE 73 ARG 0.020 0.000 ARGBK 59 ********************** 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 593 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 497 time to evaluate : 5.077 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: AA 77 MET cc_start: 0.7379 (mmm) cc_final: 0.7066 (mpp) REVERT: AA 141 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7365 (ppp) REVERT: AB 1 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7021 (ttt) REVERT: AB 39 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8307 (tpp-160) REVERT: AC 123 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9033 (pp) REVERT: AE 115 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8331 (ttt) REVERT: AE 160 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8447 (ttm) REVERT: AF 135 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: AH 6 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8289 (tmmt) REVERT: AH 60 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (pm20) REVERT: AH 87 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6856 (m-10) REVERT: AI 152 TYR cc_start: 0.7533 (m-10) cc_final: 0.7210 (m-80) REVERT: AK 17 LYS cc_start: 0.8562 (mptt) cc_final: 0.8289 (mmtt) REVERT: AK 28 LYS cc_start: 0.8915 (mtmm) cc_final: 0.8572 (mtmp) REVERT: AK 148 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7965 (mt-10) REVERT: AL 6 LYS cc_start: 0.8696 (mtmp) cc_final: 0.8472 (mttp) REVERT: AM 77 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8116 (mtm-85) REVERT: AO 44 MET cc_start: 0.7690 (mtm) cc_final: 0.7386 (mtm) REVERT: AT 289 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7494 (ttt180) REVERT: AX 28 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8125 (mmmt) REVERT: AX 54 GLU cc_start: 0.8015 (mp0) cc_final: 0.7722 (mp0) REVERT: AX 147 LYS cc_start: 0.9253 (ttmm) cc_final: 0.9048 (ttpp) REVERT: AY 77 MET cc_start: 0.7009 (mmp) cc_final: 0.6384 (mmp) REVERT: AY 88 TYR cc_start: 0.7928 (m-80) cc_final: 0.7722 (m-80) REVERT: AY 100 ASP cc_start: 0.7833 (p0) cc_final: 0.7487 (p0) REVERT: AZ 28 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8685 (mptt) REVERT: AZ 97 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8773 (tt) REVERT: AZ 149 MET cc_start: 0.9249 (mmm) cc_final: 0.9040 (tpt) REVERT: BD 6 LYS cc_start: 0.7879 (ptmt) cc_final: 0.7470 (ptpp) REVERT: BD 100 ASP cc_start: 0.6786 (t70) cc_final: 0.6132 (t0) REVERT: BE 24 MET cc_start: 0.7685 (mmm) cc_final: 0.7303 (mmm) REVERT: BE 43 VAL cc_start: 0.9197 (t) cc_final: 0.8960 (p) REVERT: BG 15 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: BG 24 MET cc_start: 0.8995 (mmm) cc_final: 0.8651 (mmm) REVERT: BH 154 ASP cc_start: 0.8736 (m-30) cc_final: 0.8415 (m-30) REVERT: BI 15 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8309 (mp10) REVERT: BI 54 GLU cc_start: 0.7777 (pm20) cc_final: 0.7414 (pm20) REVERT: BO 268 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7896 (tppt) REVERT: BO 293 ASN cc_start: 0.8559 (t0) cc_final: 0.8302 (t0) REVERT: BP 313 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8044 (pp) REVERT: BR 240 ILE cc_start: 0.6777 (mp) cc_final: 0.6450 (mt) REVERT: BR 241 ASN cc_start: 0.8470 (p0) cc_final: 0.8147 (p0) outliers start: 96 outliers final: 63 residues processed: 555 average time/residue: 1.6456 time to fit residues: 1108.1697 Evaluate side-chains 562 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 485 time to evaluate : 4.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 4 VAL Chi-restraints excluded: chain AA residue 141 MET Chi-restraints excluded: chain AB residue 1 MET Chi-restraints excluded: chain AB residue 104 LEU Chi-restraints excluded: chain AB residue 108 VAL 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 35 GLU Chi-restraints excluded: chain AD residue 54 GLU Chi-restraints excluded: chain AD residue 161 SER Chi-restraints excluded: chain AE residue 115 MET Chi-restraints excluded: chain AE residue 133 MET Chi-restraints excluded: chain AE residue 160 MET Chi-restraints excluded: chain AF residue 54 GLU Chi-restraints excluded: chain AF residue 126 THR 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 53 GLN Chi-restraints excluded: chain AJ residue 144 ASP Chi-restraints excluded: chain AM residue 77 ARG Chi-restraints excluded: chain AM residue 137 THR Chi-restraints excluded: chain AM 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 751 LEU Chi-restraints excluded: chain AQ residue 805 THR Chi-restraints excluded: chain AQ residue 884 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 39 LEU Chi-restraints excluded: chain AS residue 269 VAL Chi-restraints excluded: chain AT residue 211 ASP Chi-restraints excluded: chain AT residue 286 ILE Chi-restraints excluded: chain AT residue 289 ARG 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 47 ASN Chi-restraints excluded: chain AX residue 108 VAL Chi-restraints excluded: chain AX residue 156 ILE Chi-restraints excluded: chain AY residue 49 THR Chi-restraints excluded: chain AY residue 78 THR Chi-restraints excluded: chain AZ residue 35 GLU Chi-restraints excluded: chain AZ residue 54 GLU Chi-restraints excluded: chain AZ residue 97 LEU Chi-restraints excluded: chain BD residue 4 VAL Chi-restraints excluded: chain BD residue 49 THR Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 106 GLU 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 BH residue 141 MET Chi-restraints excluded: chain BH residue 144 ASP Chi-restraints excluded: chain BI residue 15 GLN Chi-restraints excluded: chain BI residue 58 LYS 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 212 THR Chi-restraints excluded: chain BO residue 281 ASN 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 BP residue 313 LEU Chi-restraints excluded: chain BP residue 314 ASN Chi-restraints excluded: chain BQ residue 245 SER Chi-restraints excluded: chain BR residue 204 ILE Chi-restraints excluded: chain BR residue 221 MET 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: 4.9990 chunk 456 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 395 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 429 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 440 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 ** AF 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 2 GLN ** AS 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 274 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** ** BB 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 131 GLN ** BG 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.059280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.045693 restraints weight = 169496.375| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.97 r_work: 0.3014 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 43584 Z= 0.243 Angle : 0.727 17.964 59090 Z= 0.352 Chirality : 0.040 0.209 6668 Planarity : 0.004 0.064 7602 Dihedral : 7.971 84.848 7168 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.09 % Favored : 96.85 % Rotamer: Outliers : 2.27 % Allowed : 23.21 % Favored : 74.52 % 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: 1.24 (0.12), residues: 5398 helix: 1.52 (0.08), residues: 3784 sheet: -0.29 (0.42), residues: 168 loop : -0.83 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPBO 288 HIS 0.002 0.001 HISBM 807 PHE 0.028 0.001 PHEAU 203 TYR 0.031 0.001 TYRAE 73 ARG 0.014 0.000 ARGAD 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17612.87 seconds wall clock time: 313 minutes 17.15 seconds (18797.15 seconds total)