Starting phenix.real_space_refine on Fri Feb 23 07:22:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scb_25032/02_2024/7scb_25032_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scb_25032/02_2024/7scb_25032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scb_25032/02_2024/7scb_25032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scb_25032/02_2024/7scb_25032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scb_25032/02_2024/7scb_25032_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scb_25032/02_2024/7scb_25032_updated.pdb" } resolution = 2.5 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= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 194 5.16 5 C 23522 2.51 5 N 6298 2.21 5 O 7215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BE PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37229 Number of models: 1 Model: "" Number of chains: 54 Chain: "AA" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AB" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AC" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AD" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AE" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1254 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain: "AF" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AH" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AI" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AJ" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AK" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1322 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "AL" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AN" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AO" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AP" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AQ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AR" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AS" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AU" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AV" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AW" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AX" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AY" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AZ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BB" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "BC" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "BE" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5124 Classifications: {'peptide': 647} Link IDs: {'PTRANS': 37, 'TRANS': 609} Chain breaks: 1 Chain: "BG" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 451 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain: "BH" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1269 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain: "BI" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 277 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Chain: "AA" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AI" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AK" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AO" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AQ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AS" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AU" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AW" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AY" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'45D': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.21, per 1000 atoms: 0.54 Number of scatterers: 37229 At special positions: 0 Unit cell: (159.6, 144.9, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 194 16.00 O 7215 8.00 N 6298 7.00 C 23522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 15.05 Conformation dependent library (CDL) restraints added in 6.8 seconds 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8734 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 249 helices and 5 sheets defined 69.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.17 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 13 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 removed outlier: 3.652A pdb=" N VALAA 51 " --> pdb=" O ARGAA 47 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALAAA 54 " --> pdb=" O ILEAA 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHEAA 59 " --> pdb=" O GLYAA 55 " (cutoff:3.500A) Processing helix chain 'AA' and resid 75 through 98 removed outlier: 3.518A pdb=" N ALAAA 79 " --> pdb=" O GLUAA 75 " (cutoff:3.500A) Processing helix chain 'AA' and resid 102 through 108 Processing helix chain 'AA' and resid 112 through 119 Processing helix chain 'AA' and resid 123 through 140 removed outlier: 3.587A pdb=" N GLUAA 135 " --> pdb=" O ARGAA 131 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLYAA 139 " --> pdb=" O GLUAA 135 " (cutoff:3.500A) Processing helix chain 'AA' and resid 143 through 159 removed outlier: 3.957A pdb=" N ALAAA 151 " --> pdb=" O ALAAA 147 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYRAA 152 " --> pdb=" O GLUAA 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VALAA 156 " --> pdb=" O TYRAA 152 " (cutoff:3.500A) Processing helix chain 'AB' and resid 4 through 15 removed outlier: 3.723A pdb=" N VALAB 8 " --> pdb=" O ALAAB 4 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLNAB 15 " --> pdb=" O SERAB 11 " (cutoff:3.500A) Processing helix chain 'AB' and resid 21 through 32 removed outlier: 3.612A pdb=" N ASPAB 25 " --> pdb=" O GLYAB 21 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYSAB 26 " --> pdb=" O ALAAB 22 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEUAB 27 " --> pdb=" O ALAAB 23 " (cutoff:3.500A) Processing helix chain 'AB' and resid 34 through 46 Processing helix chain 'AB' and resid 48 through 59 removed outlier: 4.032A pdb=" N VALAB 52 " --> pdb=" O ALAAB 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALAAB 57 " --> pdb=" O LYSAB 53 " (cutoff:3.500A) Processing helix chain 'AB' and resid 75 through 98 removed outlier: 3.975A pdb=" N ALAAB 92 " --> pdb=" O TYRAB 88 " (cutoff:3.500A) Processing helix chain 'AB' and resid 103 through 106 No H-bonds generated for 'chain 'AB' and resid 103 through 106' Processing helix chain 'AB' and resid 112 through 119 Processing helix chain 'AB' and resid 123 through 141 removed outlier: 3.501A pdb=" N SERAB 139 " --> pdb=" O GLUAB 135 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEUAB 140 " --> pdb=" O VALAB 136 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VALAB 141 " --> pdb=" O THRAB 137 " (cutoff:3.500A) Processing helix chain 'AB' and resid 143 through 160 removed outlier: 3.880A pdb=" N TYRAB 152 " --> pdb=" O GLUAB 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 3 through 14 removed outlier: 3.646A pdb=" N ILEAC 8 " --> pdb=" O VALAC 4 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASNAC 10 " --> pdb=" O LYSAC 6 " (cutoff:3.500A) Processing helix chain 'AC' and resid 20 through 45 removed outlier: 3.657A pdb=" N ARGAC 25 " --> pdb=" O GLYAC 21 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALAAC 34 " --> pdb=" O VALAC 30 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALAAC 35 " --> pdb=" O THRAC 31 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARGAC 36 " --> pdb=" O GLYAC 32 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILEAC 39 " --> pdb=" O ALAAC 35 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALAAC 40 " --> pdb=" O ARGAC 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THRAC 42 " --> pdb=" O ARGAC 38 " (cutoff:3.500A) Processing helix chain 'AC' and resid 47 through 61 removed outlier: 3.811A pdb=" N VALAC 51 " --> pdb=" O ARGAC 47 " (cutoff:3.500A) 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 76 through 98 removed outlier: 3.748A pdb=" N THRAC 80 " --> pdb=" O GLUAC 76 " (cutoff:3.500A) Processing helix chain 'AC' and resid 102 through 108 Processing helix chain 'AC' and resid 113 through 117 Processing helix chain 'AC' and resid 123 through 140 removed outlier: 3.598A pdb=" N VALAC 130 " --> pdb=" O VALAC 126 " (cutoff:3.500A) Processing helix chain 'AC' and resid 143 through 159 removed outlier: 4.166A pdb=" N GLUAC 148 " --> pdb=" O ASPAC 144 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALAAC 149 " --> pdb=" O ASPAC 145 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALAAC 151 " --> pdb=" O ALAAC 147 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYRAC 152 " --> pdb=" O GLUAC 148 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHEAC 155 " --> pdb=" O ALAAC 151 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VALAC 156 " --> pdb=" O TYRAC 152 " (cutoff:3.500A) Processing helix chain 'AD' and resid 5 through 13 removed outlier: 3.528A pdb=" N ALAAD 12 " --> pdb=" O VALAD 8 " (cutoff:3.500A) Processing helix chain 'AD' and resid 21 through 32 removed outlier: 4.154A pdb=" N LYSAD 26 " --> pdb=" O ALAAD 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SERAD 29 " --> pdb=" O ASPAD 25 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYRAD 30 " --> pdb=" O LYSAD 26 " (cutoff:3.500A) Processing helix chain 'AD' and resid 34 through 46 Processing helix chain 'AD' and resid 48 through 57 removed outlier: 4.179A pdb=" N VALAD 52 " --> pdb=" O ALAAD 48 " (cutoff:3.500A) Processing helix chain 'AD' and resid 75 through 98 Processing helix chain 'AD' and resid 102 through 107 Processing helix chain 'AD' and resid 114 through 119 Processing helix chain 'AD' and resid 123 through 141 removed outlier: 3.707A pdb=" N LYSAD 134 " --> pdb=" O ILEAD 130 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLUAD 135 " --> pdb=" O GLNAD 131 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VALAD 136 " --> pdb=" O ALAAD 132 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SERAD 139 " --> pdb=" O GLUAD 135 " (cutoff:3.500A) Processing helix chain 'AD' and resid 143 through 160 removed outlier: 3.716A pdb=" N GLUAD 148 " --> pdb=" O ASPAD 144 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VALAD 151 " --> pdb=" O LYSAD 147 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYRAD 152 " --> pdb=" O GLUAD 148 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLYAD 159 " --> pdb=" O TYRAD 155 " (cutoff:3.500A) Processing helix chain 'AE' and resid 3 through 13 Processing helix chain 'AE' and resid 20 through 44 removed outlier: 3.648A pdb=" N PHEAE 29 " --> pdb=" O GLYAE 25 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THRAE 31 " --> pdb=" O GLNAE 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THRAE 32 " --> pdb=" O ALAAE 28 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALAAE 34 " --> pdb=" O LEUAE 30 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLNAE 35 " --> pdb=" O THRAE 31 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARGAE 38 " --> pdb=" O ALAAE 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALAAE 40 " --> pdb=" O ARGAE 36 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLUAE 41 " --> pdb=" O ILEAE 37 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THRAE 42 " --> pdb=" O ARGAE 38 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEUAE 43 " --> pdb=" O ILEAE 39 " (cutoff:3.500A) Processing helix chain 'AE' and resid 47 through 61 removed outlier: 3.598A pdb=" N LYSAE 60 " --> pdb=" O LYSAE 56 " (cutoff:3.500A) Processing helix chain 'AE' and resid 75 through 98 removed outlier: 3.679A pdb=" N GLNAE 80 " --> pdb=" O ARGAE 76 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEUAE 82 " --> pdb=" O TYRAE 78 " (cutoff:3.500A) Processing helix chain 'AE' and resid 102 through 108 removed outlier: 3.769A pdb=" N THRAE 107 " --> pdb=" O PROAE 103 " (cutoff:3.500A) Processing helix chain 'AE' and resid 113 through 117 Processing helix chain 'AE' and resid 123 through 140 removed outlier: 4.116A pdb=" N ASPAE 128 " --> pdb=" O PROAE 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALAAE 129 " --> pdb=" O GLYAE 125 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THRAE 131 " --> pdb=" O VALAE 127 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VALAE 132 " --> pdb=" O ASPAE 128 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEUAE 140 " --> pdb=" O ALAAE 136 " (cutoff:3.500A) Processing helix chain 'AE' and resid 143 through 160 removed outlier: 3.749A pdb=" N ASNAE 147 " --> pdb=" O ALAAE 143 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLUAE 148 " --> pdb=" O GLUAE 144 " (cutoff:3.500A) Proline residue: AE 151 - end of helix removed outlier: 3.698A pdb=" N ILEAE 156 " --> pdb=" O TYRAE 152 " (cutoff:3.500A) Processing helix chain 'AF' and resid 4 through 15 removed outlier: 3.877A pdb=" N VALAF 8 " --> pdb=" O ALAAF 4 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILEAF 9 " --> pdb=" O ILEAF 5 " (cutoff:3.500A) Processing helix chain 'AF' and resid 21 through 32 removed outlier: 5.293A pdb=" N LYSAF 26 " --> pdb=" O ALAAF 22 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEUAF 27 " --> pdb=" O ALAAF 23 " (cutoff:3.500A) Processing helix chain 'AF' and resid 34 through 46 removed outlier: 3.557A pdb=" N ARGAF 39 " --> pdb=" O GLUAF 35 " (cutoff:3.500A) Processing helix chain 'AF' and resid 48 through 59 removed outlier: 3.975A pdb=" N VALAF 52 " --> pdb=" O ALAAF 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYSAF 53 " --> pdb=" O ALAAF 49 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYSAF 58 " --> pdb=" O GLUAF 54 " (cutoff:3.500A) Processing helix chain 'AF' and resid 75 through 98 Processing helix chain 'AF' and resid 103 through 106 No H-bonds generated for 'chain 'AF' and resid 103 through 106' Processing helix chain 'AF' and resid 112 through 119 removed outlier: 3.728A pdb=" N ASNAF 117 " --> pdb=" O LYSAF 113 " (cutoff:3.500A) Processing helix chain 'AF' and resid 123 through 140 Processing helix chain 'AF' and resid 143 through 160 removed outlier: 3.611A pdb=" N LYSAF 147 " --> pdb=" O ALAAF 143 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLUAF 148 " --> pdb=" O ASPAF 144 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VALAF 151 " --> pdb=" O LYSAF 147 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYRAF 152 " --> pdb=" O GLUAF 148 " (cutoff:3.500A) Processing helix chain 'AH' and resid 3 through 13 Processing helix chain 'AH' and resid 20 through 45 removed outlier: 4.289A pdb=" N ARGAH 25 " --> pdb=" O GLYAH 21 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLYAH 33 " --> pdb=" O PHEAH 29 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALAAH 34 " --> pdb=" O VALAH 30 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALAAH 35 " --> pdb=" O THRAH 31 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARGAH 36 " --> pdb=" O GLYAH 32 " (cutoff:3.500A) Processing helix chain 'AH' and resid 47 through 61 removed outlier: 3.673A pdb=" N VALAH 51 " --> pdb=" O ARGAH 47 " (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 76 through 98 Processing helix chain 'AH' and resid 102 through 108 removed outlier: 3.569A pdb=" N ILEAH 107 " --> pdb=" O PROAH 103 " (cutoff:3.500A) Processing helix chain 'AH' and resid 112 through 119 Processing helix chain 'AH' and resid 123 through 139 Processing helix chain 'AH' and resid 143 through 160 removed outlier: 3.921A pdb=" N TYRAH 152 " --> pdb=" O GLUAH 148 " (cutoff:3.500A) Processing helix chain 'AI' and resid 4 through 15 removed outlier: 3.601A pdb=" N VALAI 8 " --> pdb=" O ALAAI 4 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLNAI 15 " --> pdb=" O SERAI 11 " (cutoff:3.500A) Processing helix chain 'AI' and resid 21 through 46 removed outlier: 3.837A pdb=" N LYSAI 26 " --> pdb=" O ALAAI 22 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEUAI 27 " --> pdb=" O ALAAI 23 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLUAI 35 " --> pdb=" O PHEAI 31 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEUAI 36 " --> pdb=" O ALAAI 32 " (cutoff:3.500A) Processing helix chain 'AI' and resid 48 through 59 removed outlier: 3.868A pdb=" N VALAI 52 " --> pdb=" O ALAAI 48 " (cutoff:3.500A) Processing helix chain 'AI' and resid 75 through 98 Processing helix chain 'AI' and resid 104 through 107 No H-bonds generated for 'chain 'AI' and resid 104 through 107' Processing helix chain 'AI' and resid 113 through 119 Processing helix chain 'AI' and resid 123 through 140 removed outlier: 3.765A pdb=" N GLNAI 128 " --> pdb=" O SERAI 124 " (cutoff:3.500A) Processing helix chain 'AI' and resid 143 through 160 removed outlier: 3.755A pdb=" N GLUAI 148 " --> pdb=" O ASPAI 144 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYRAI 152 " --> pdb=" O GLUAI 148 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 3 through 14 removed outlier: 3.802A pdb=" N GLUAJ 14 " --> pdb=" O ASNAJ 10 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 20 through 45 removed outlier: 4.518A pdb=" N ALAAJ 34 " --> pdb=" O VALAJ 30 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALAAJ 35 " --> pdb=" O THRAJ 31 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 47 through 61 removed outlier: 3.587A pdb=" N VALAJ 51 " --> pdb=" O ARGAJ 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYSAJ 52 " --> pdb=" O GLUAJ 48 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 75 through 98 Processing helix chain 'AJ' and resid 102 through 108 Processing helix chain 'AJ' and resid 112 through 119 Processing helix chain 'AJ' and resid 123 through 138 Processing helix chain 'AJ' and resid 143 through 160 removed outlier: 3.812A pdb=" N ALAAJ 151 " --> pdb=" O ALAAJ 147 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYRAJ 152 " --> pdb=" O GLUAJ 148 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VALAJ 156 " --> pdb=" O TYRAJ 152 " (cutoff:3.500A) Processing helix chain 'AK' and resid 4 through 15 removed outlier: 3.883A pdb=" N THRAK 15 " --> pdb=" O ASNAK 11 " (cutoff:3.500A) Processing helix chain 'AK' and resid 21 through 46 removed outlier: 4.409A pdb=" N SERAK 35 " --> pdb=" O PHEAK 31 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALAAK 36 " --> pdb=" O GLUAK 32 " (cutoff:3.500A) Processing helix chain 'AK' and resid 48 through 62 removed outlier: 3.639A pdb=" N VALAK 52 " --> pdb=" O SERAK 48 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLUAK 61 " --> pdb=" O ALAAK 57 " (cutoff:3.500A) Processing helix chain 'AK' and resid 76 through 99 removed outlier: 3.826A pdb=" N ILEAK 98 " --> pdb=" O SERAK 94 " (cutoff:3.500A) Processing helix chain 'AK' and resid 103 through 107 Processing helix chain 'AK' and resid 114 through 120 Processing helix chain 'AK' and resid 125 through 144 Processing helix chain 'AK' and resid 151 through 164 removed outlier: 3.634A pdb=" N ALAAK 154 " --> pdb=" O ASPAK 151 " (cutoff:3.500A) Proline residue: AK 156 - end of helix removed outlier: 4.142A pdb=" N GLUAK 163 " --> pdb=" O METAK 160 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEUAK 164 " --> pdb=" O THRAK 161 " (cutoff:3.500A) Processing helix chain 'AL' and resid 4 through 15 Processing helix chain 'AL' and resid 22 through 46 removed outlier: 3.578A pdb=" N LYSAL 26 " --> pdb=" O ALAAL 22 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLUAL 35 " --> pdb=" O PHEAL 31 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEUAL 36 " --> pdb=" O ALAAL 32 " (cutoff:3.500A) Processing helix chain 'AL' and resid 48 through 59 removed outlier: 3.744A pdb=" N VALAL 52 " --> pdb=" O ALAAL 48 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYSAL 53 " --> pdb=" O ALAAL 49 " (cutoff:3.500A) Processing helix chain 'AL' and resid 75 through 98 Processing helix chain 'AL' and resid 102 through 106 Processing helix chain 'AL' and resid 112 through 119 removed outlier: 3.741A pdb=" N SERAL 118 " --> pdb=" O GLUAL 114 " (cutoff:3.500A) Processing helix chain 'AL' and resid 123 through 140 Processing helix chain 'AL' and resid 143 through 160 removed outlier: 4.586A pdb=" N TYRAL 152 " --> pdb=" O GLUAL 148 " (cutoff:3.500A) Processing helix chain 'AN' and resid 3 through 13 Processing helix chain 'AN' and resid 20 through 31 Processing helix chain 'AN' and resid 33 through 45 removed outlier: 3.521A pdb=" N ILEAN 39 " --> pdb=" O ALAAN 35 " (cutoff:3.500A) Processing helix chain 'AN' and resid 50 through 61 Processing helix chain 'AN' and resid 75 through 98 Processing helix chain 'AN' and resid 102 through 108 removed outlier: 4.890A pdb=" N ILEAN 107 " --> pdb=" O PROAN 103 " (cutoff:3.500A) Processing helix chain 'AN' and resid 113 through 119 removed outlier: 3.745A pdb=" N SERAN 118 " --> pdb=" O GLUAN 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEUAN 119 " --> pdb=" O METAN 115 " (cutoff:3.500A) Processing helix chain 'AN' and resid 123 through 139 Processing helix chain 'AN' and resid 144 through 160 removed outlier: 3.932A pdb=" N GLUAN 148 " --> pdb=" O ASPAN 144 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYRAN 152 " --> pdb=" O GLUAN 148 " (cutoff:3.500A) Processing helix chain 'AO' and resid 4 through 15 removed outlier: 3.617A pdb=" N VALAO 8 " --> pdb=" O ALAAO 4 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLNAO 15 " --> pdb=" O SERAO 11 " (cutoff:3.500A) Processing helix chain 'AO' and resid 21 through 46 removed outlier: 4.028A pdb=" N GLUAO 35 " --> pdb=" O PHEAO 31 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEUAO 36 " --> pdb=" O ALAAO 32 " (cutoff:3.500A) Processing helix chain 'AO' and resid 49 through 59 Processing helix chain 'AO' and resid 75 through 98 Processing helix chain 'AO' and resid 102 through 106 Processing helix chain 'AO' and resid 112 through 119 Processing helix chain 'AO' and resid 123 through 140 Processing helix chain 'AO' and resid 145 through 159 removed outlier: 4.306A pdb=" N TYRAO 152 " --> pdb=" O GLUAO 148 " (cutoff:3.500A) Processing helix chain 'AP' and resid 3 through 13 Processing helix chain 'AP' and resid 20 through 45 removed outlier: 4.986A pdb=" N ALAAP 34 " --> pdb=" O VALAP 30 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALAAP 35 " --> pdb=" O THRAP 31 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARGAP 36 " --> pdb=" O GLYAP 32 " (cutoff:3.500A) Processing helix chain 'AP' and resid 47 through 61 removed outlier: 3.533A pdb=" N LYSAP 52 " --> pdb=" O GLUAP 48 " (cutoff:3.500A) Processing helix chain 'AP' and resid 75 through 98 removed outlier: 3.611A pdb=" N ALAAP 79 " --> pdb=" O GLUAP 75 " (cutoff:3.500A) Processing helix chain 'AP' and resid 102 through 108 Processing helix chain 'AP' and resid 113 through 119 Processing helix chain 'AP' and resid 123 through 138 Processing helix chain 'AP' and resid 143 through 160 removed outlier: 3.693A pdb=" N ALAAP 151 " --> pdb=" O ALAAP 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYRAP 152 " --> pdb=" O GLUAP 148 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHEAP 155 " --> pdb=" O ALAAP 151 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 4 through 15 Processing helix chain 'AQ' and resid 21 through 32 removed outlier: 3.554A pdb=" N TYRAQ 30 " --> pdb=" O LYSAQ 26 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 34 through 46 Processing helix chain 'AQ' and resid 48 through 59 removed outlier: 3.841A pdb=" N VALAQ 52 " --> pdb=" O ALAAQ 48 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSAQ 58 " --> pdb=" O GLUAQ 54 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 75 through 98 Processing helix chain 'AQ' and resid 102 through 107 Processing helix chain 'AQ' and resid 113 through 119 Processing helix chain 'AQ' and resid 123 through 140 Processing helix chain 'AQ' and resid 144 through 160 removed outlier: 3.895A pdb=" N TYRAQ 152 " --> pdb=" O GLUAQ 148 " (cutoff:3.500A) Processing helix chain 'AR' and resid 3 through 13 Processing helix chain 'AR' and resid 20 through 45 removed outlier: 4.782A pdb=" N ALAAR 34 " --> pdb=" O VALAR 30 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALAAR 35 " --> pdb=" O THRAR 31 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARGAR 36 " --> pdb=" O GLYAR 32 " (cutoff:3.500A) Processing helix chain 'AR' and resid 47 through 61 removed outlier: 3.664A pdb=" N VALAR 51 " --> pdb=" O ARGAR 47 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSAR 52 " --> pdb=" O GLUAR 48 " (cutoff:3.500A) Processing helix chain 'AR' and resid 75 through 98 Processing helix chain 'AR' and resid 102 through 108 Processing helix chain 'AR' and resid 112 through 119 Processing helix chain 'AR' and resid 123 through 140 removed outlier: 3.532A pdb=" N GLUAR 135 " --> pdb=" O ARGAR 131 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEUAR 140 " --> pdb=" O VALAR 136 " (cutoff:3.500A) Processing helix chain 'AR' and resid 143 through 147 Processing helix chain 'AR' and resid 150 through 160 removed outlier: 3.611A pdb=" N VALAR 156 " --> pdb=" O TYRAR 152 " (cutoff:3.500A) Processing helix chain 'AS' and resid 4 through 15 removed outlier: 3.529A pdb=" N VALAS 8 " --> pdb=" O ALAAS 4 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLNAS 15 " --> pdb=" O SERAS 11 " (cutoff:3.500A) Processing helix chain 'AS' and resid 21 through 32 Processing helix chain 'AS' and resid 35 through 46 removed outlier: 3.504A pdb=" N VALAS 43 " --> pdb=" O ARGAS 39 " (cutoff:3.500A) Processing helix chain 'AS' and resid 48 through 59 removed outlier: 4.039A pdb=" N VALAS 52 " --> pdb=" O ALAAS 48 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SERAS 59 " --> pdb=" O ALAAS 55 " (cutoff:3.500A) Processing helix chain 'AS' and resid 75 through 98 Processing helix chain 'AS' and resid 103 through 107 Processing helix chain 'AS' and resid 113 through 119 Processing helix chain 'AS' and resid 123 through 141 removed outlier: 3.708A pdb=" N GLUAS 135 " --> pdb=" O GLNAS 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VALAS 136 " --> pdb=" O ALAAS 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEUAS 140 " --> pdb=" O VALAS 136 " (cutoff:3.500A) Processing helix chain 'AS' and resid 144 through 160 removed outlier: 3.597A pdb=" N TYRAS 152 " --> pdb=" O GLUAS 148 " (cutoff:3.500A) Processing helix chain 'AU' and resid 3 through 13 Processing helix chain 'AU' and resid 20 through 31 Processing helix chain 'AU' and resid 33 through 45 Processing helix chain 'AU' and resid 47 through 61 removed outlier: 3.665A pdb=" N VALAU 51 " --> pdb=" O ARGAU 47 " (cutoff:3.500A) Processing helix chain 'AU' and resid 63 through 65 No H-bonds generated for 'chain 'AU' and resid 63 through 65' Processing helix chain 'AU' and resid 75 through 98 removed outlier: 3.595A pdb=" N ALAAU 79 " --> pdb=" O GLUAU 75 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VALAU 97 " --> pdb=" O THRAU 93 " (cutoff:3.500A) Processing helix chain 'AU' and resid 102 through 108 Processing helix chain 'AU' and resid 112 through 119 removed outlier: 3.623A pdb=" N ARGAU 117 " --> pdb=" O ARGAU 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEUAU 119 " --> pdb=" O METAU 115 " (cutoff:3.500A) Processing helix chain 'AU' and resid 123 through 140 Processing helix chain 'AU' and resid 143 through 160 removed outlier: 3.873A pdb=" N GLUAU 148 " --> pdb=" O ASPAU 144 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAU 151 " --> pdb=" O ALAAU 147 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYRAU 152 " --> pdb=" O GLUAU 148 " (cutoff:3.500A) Processing helix chain 'AV' and resid 4 through 15 removed outlier: 3.901A pdb=" N GLNAV 15 " --> pdb=" O SERAV 11 " (cutoff:3.500A) Processing helix chain 'AV' and resid 21 through 32 removed outlier: 3.646A pdb=" N LYSAV 26 " --> pdb=" O ALAAV 22 " (cutoff:3.500A) Processing helix chain 'AV' and resid 34 through 46 Processing helix chain 'AV' and resid 48 through 59 removed outlier: 3.878A pdb=" N VALAV 52 " --> pdb=" O ALAAV 48 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAV 56 " --> pdb=" O VALAV 52 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALAAV 57 " --> pdb=" O LYSAV 53 " (cutoff:3.500A) Processing helix chain 'AV' and resid 75 through 98 Processing helix chain 'AV' and resid 104 through 107 No H-bonds generated for 'chain 'AV' and resid 104 through 107' Processing helix chain 'AV' and resid 113 through 118 Processing helix chain 'AV' and resid 123 through 140 removed outlier: 4.013A pdb=" N GLUAV 135 " --> pdb=" O GLNAV 131 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VALAV 136 " --> pdb=" O ALAAV 132 " (cutoff:3.500A) Processing helix chain 'AV' and resid 144 through 160 removed outlier: 3.744A pdb=" N TYRAV 152 " --> pdb=" O GLUAV 148 " (cutoff:3.500A) Processing helix chain 'AW' and resid 3 through 13 Processing helix chain 'AW' and resid 20 through 31 Processing helix chain 'AW' and resid 33 through 45 Processing helix chain 'AW' and resid 47 through 61 removed outlier: 3.528A pdb=" N VALAW 51 " --> pdb=" O ARGAW 47 " (cutoff:3.500A) Processing helix chain 'AW' and resid 75 through 98 removed outlier: 3.600A pdb=" N VALAW 97 " --> pdb=" O THRAW 93 " (cutoff:3.500A) Processing helix chain 'AW' and resid 102 through 108 removed outlier: 3.559A pdb=" N ILEAW 107 " --> pdb=" O PROAW 103 " (cutoff:3.500A) Processing helix chain 'AW' and resid 115 through 119 Processing helix chain 'AW' and resid 123 through 140 Processing helix chain 'AW' and resid 143 through 160 removed outlier: 4.177A pdb=" N GLUAW 148 " --> pdb=" O ASPAW 144 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALAAW 151 " --> pdb=" O ALAAW 147 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYRAW 152 " --> pdb=" O GLUAW 148 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHEAW 155 " --> pdb=" O ALAAW 151 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VALAW 156 " --> pdb=" O TYRAW 152 " (cutoff:3.500A) Processing helix chain 'AX' and resid 5 through 15 removed outlier: 4.167A pdb=" N GLNAX 15 " --> pdb=" O SERAX 11 " (cutoff:3.500A) Processing helix chain 'AX' and resid 21 through 46 removed outlier: 4.206A pdb=" N LYSAX 26 " --> pdb=" O ALAAX 22 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEUAX 27 " --> pdb=" O ALAAX 23 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLUAX 35 " --> pdb=" O PHEAX 31 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEUAX 36 " --> pdb=" O ALAAX 32 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARGAX 39 " --> pdb=" O GLUAX 35 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VALAX 43 " --> pdb=" O ARGAX 39 " (cutoff:3.500A) Processing helix chain 'AX' and resid 48 through 59 removed outlier: 3.680A 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 113 through 119 Processing helix chain 'AX' and resid 123 through 141 Processing helix chain 'AX' and resid 143 through 160 removed outlier: 4.319A pdb=" N TYRAX 152 " --> pdb=" O GLUAX 148 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYSAX 157 " --> pdb=" O LEUAX 153 " (cutoff:3.500A) Processing helix chain 'AY' and resid 3 through 13 Processing helix chain 'AY' and resid 20 through 31 Processing helix chain 'AY' and resid 33 through 45 removed outlier: 3.841A pdb=" N ILEAY 39 " --> pdb=" O ALAAY 35 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALAAY 40 " --> pdb=" O ARGAY 36 " (cutoff:3.500A) Processing helix chain 'AY' and resid 47 through 61 removed outlier: 3.905A pdb=" N VALAY 51 " --> pdb=" O ARGAY 47 " (cutoff:3.500A) Processing helix chain 'AY' and resid 75 through 98 Processing helix chain 'AY' and resid 102 through 108 removed outlier: 3.625A pdb=" N ILEAY 107 " --> pdb=" O PROAY 103 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLYAY 108 " --> pdb=" O ILEAY 104 " (cutoff:3.500A) Processing helix chain 'AY' and resid 113 through 119 Processing helix chain 'AY' and resid 123 through 139 Processing helix chain 'AY' and resid 143 through 160 removed outlier: 3.808A pdb=" N ALAAY 151 " --> pdb=" O ALAAY 147 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYRAY 152 " --> pdb=" O GLUAY 148 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHEAY 155 " --> pdb=" O ALAAY 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAY 156 " --> pdb=" O TYRAY 152 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 4 through 15 removed outlier: 3.773A pdb=" N GLNAZ 15 " --> pdb=" O SERAZ 11 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 21 through 32 removed outlier: 3.541A pdb=" N LYSAZ 26 " --> pdb=" O ALAAZ 22 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 34 through 46 Processing helix chain 'AZ' and resid 48 through 59 removed outlier: 3.794A pdb=" N VALAZ 52 " --> pdb=" O ALAAZ 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALAAZ 57 " --> pdb=" O LYSAZ 53 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 75 through 98 Processing helix chain 'AZ' and resid 103 through 106 No H-bonds generated for 'chain 'AZ' and resid 103 through 106' Processing helix chain 'AZ' and resid 112 through 119 Processing helix chain 'AZ' and resid 123 through 141 removed outlier: 3.575A pdb=" N GLUAZ 135 " --> pdb=" O GLNAZ 131 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 143 through 160 removed outlier: 3.852A pdb=" N GLUAZ 148 " --> pdb=" O ASPAZ 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYRAZ 152 " --> pdb=" O GLUAZ 148 " (cutoff:3.500A) Processing helix chain 'BB' and resid 15 through 18 No H-bonds generated for 'chain 'BB' and resid 15 through 18' Processing helix chain 'BB' and resid 33 through 45 removed outlier: 4.479A pdb=" N PHEBB 37 " --> pdb=" O TYRBB 33 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARGBB 38 " --> pdb=" O ASPBB 34 " (cutoff:3.500A) Processing helix chain 'BC' and resid 22 through 25 No H-bonds generated for 'chain 'BC' and resid 22 through 25' Processing helix chain 'BC' and resid 36 through 46 Processing helix chain 'BE' and resid 20 through 29 removed outlier: 3.658A pdb=" N GLNBE 27 " --> pdb=" O SERBE 23 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALABE 28 " --> pdb=" O ALABE 24 " (cutoff:3.500A) Processing helix chain 'BE' and resid 37 through 62 removed outlier: 3.611A pdb=" N ASNBE 41 " --> pdb=" O GLYBE 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEUBE 43 " --> pdb=" O GLUBE 39 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYRBE 46 " --> pdb=" O GLUBE 42 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALABE 51 " --> pdb=" O PHEBE 47 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEUBE 52 " --> pdb=" O GLNBE 48 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLUBE 55 " --> pdb=" O ALABE 51 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THRBE 59 " --> pdb=" O GLUBE 55 " (cutoff:3.500A) Processing helix chain 'BE' and resid 64 through 75 removed outlier: 3.625A pdb=" N ARGBE 74 " --> pdb=" O ARGBE 70 " (cutoff:3.500A) Processing helix chain 'BE' and resid 81 through 83 No H-bonds generated for 'chain 'BE' and resid 81 through 83' Processing helix chain 'BE' and resid 141 through 144 No H-bonds generated for 'chain 'BE' and resid 141 through 144' Processing helix chain 'BE' and resid 146 through 169 removed outlier: 3.602A pdb=" N LEUBE 160 " --> pdb=" O METBE 156 " (cutoff:3.500A) Processing helix chain 'BE' and resid 173 through 186 removed outlier: 3.717A pdb=" N ASNBE 178 " --> pdb=" O ILEBE 174 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLYBE 181 " --> pdb=" O VALBE 177 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEUBE 182 " --> pdb=" O ASNBE 178 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYSBE 183 " --> pdb=" O THRBE 179 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLUBE 184 " --> pdb=" O ARGBE 180 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VALBE 185 " --> pdb=" O GLYBE 181 " (cutoff:3.500A) Processing helix chain 'BE' and resid 192 through 210 removed outlier: 3.815A pdb=" N VALBE 197 " --> pdb=" O ASPBE 193 " (cutoff:3.500A) Processing helix chain 'BE' and resid 217 through 232 Processing helix chain 'BE' and resid 257 through 259 No H-bonds generated for 'chain 'BE' and resid 257 through 259' Processing helix chain 'BE' and resid 275 through 289 Processing helix chain 'BE' and resid 294 through 297 No H-bonds generated for 'chain 'BE' and resid 294 through 297' Processing helix chain 'BE' and resid 303 through 311 removed outlier: 4.067A pdb=" N GLNBE 308 " --> pdb=" O TYRBE 304 " (cutoff:3.500A) Processing helix chain 'BE' and resid 316 through 324 Processing helix chain 'BE' and resid 327 through 333 removed outlier: 4.058A pdb=" N GLNBE 332 " --> pdb=" O LEUBE 328 " (cutoff:3.500A) Processing helix chain 'BE' and resid 339 through 350 removed outlier: 3.751A pdb=" N ARGBE 348 " --> pdb=" O GLUBE 344 " (cutoff:3.500A) Processing helix chain 'BE' and resid 358 through 370 Processing helix chain 'BE' and resid 373 through 381 Processing helix chain 'BE' and resid 386 through 389 No H-bonds generated for 'chain 'BE' and resid 386 through 389' Processing helix chain 'BE' and resid 411 through 418 removed outlier: 3.588A pdb=" N LEUBE 417 " --> pdb=" O METBE 413 " (cutoff:3.500A) Processing helix chain 'BE' and resid 422 through 424 No H-bonds generated for 'chain 'BE' and resid 422 through 424' Processing helix chain 'BE' and resid 430 through 438 removed outlier: 3.990A pdb=" N ASPBE 438 " --> pdb=" O PHEBE 434 " (cutoff:3.500A) Processing helix chain 'BE' and resid 490 through 492 No H-bonds generated for 'chain 'BE' and resid 490 through 492' Processing helix chain 'BE' and resid 537 through 550 Processing helix chain 'BE' and resid 557 through 559 No H-bonds generated for 'chain 'BE' and resid 557 through 559' Processing helix chain 'BE' and resid 562 through 570 Processing helix chain 'BE' and resid 575 through 583 Processing helix chain 'BE' and resid 586 through 591 Processing helix chain 'BE' and resid 598 through 609 Processing helix chain 'BE' and resid 617 through 629 removed outlier: 3.566A pdb=" N GLNBE 622 " --> pdb=" O GLNBE 618 " (cutoff:3.500A) Processing helix chain 'BE' and resid 632 through 640 Processing helix chain 'BE' and resid 643 through 648 Processing helix chain 'BE' and resid 662 through 668 Processing helix chain 'BG' and resid 196 through 201 removed outlier: 3.519A pdb=" N ARGBG 201 " --> pdb=" O GLNBG 197 " (cutoff:3.500A) Processing helix chain 'BG' and resid 221 through 224 No H-bonds generated for 'chain 'BG' and resid 221 through 224' Processing helix chain 'BG' and resid 242 through 245 No H-bonds generated for 'chain 'BG' and resid 242 through 245' Processing helix chain 'BH' and resid 21 through 30 Processing helix chain 'BH' and resid 33 through 45 removed outlier: 3.604A pdb=" N TRPBH 41 " --> pdb=" O LEUBH 37 " (cutoff:3.500A) Processing helix chain 'BH' and resid 65 through 73 Processing helix chain 'BH' and resid 76 through 88 removed outlier: 3.657A pdb=" N THRBH 80 " --> pdb=" O PROBH 76 " (cutoff:3.500A) Processing helix chain 'BH' and resid 93 through 98 Processing helix chain 'BH' and resid 103 through 119 Processing helix chain 'BH' and resid 133 through 144 removed outlier: 3.503A pdb=" N VALBH 138 " --> pdb=" O ASNBH 134 " (cutoff:3.500A) Processing helix chain 'BH' and resid 147 through 159 removed outlier: 3.669A pdb=" N ILEBH 151 " --> pdb=" O SERBH 147 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THRBH 152 " --> pdb=" O GLYBH 148 " (cutoff:3.500A) Processing helix chain 'BI' and resid 105 through 115 removed outlier: 3.563A pdb=" N ASNBI 108 " --> pdb=" O PROBI 105 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARGBI 109 " --> pdb=" O SERBI 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYSBI 111 " --> pdb=" O ASNBI 108 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'BB' and resid 26 through 32 removed outlier: 6.478A pdb=" N ARGBB 5 " --> pdb=" O LEUBB 55 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEUBB 55 " --> pdb=" O ARGBB 5 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THRBB 7 " --> pdb=" O VALBB 53 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VALBB 53 " --> pdb=" O THRBB 7 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'BC' and resid 26 through 32 Processing sheet with id= C, first strand: chain 'BC' and resid 3 through 7 removed outlier: 3.570A pdb=" N METBC 3 " --> pdb=" O THRBC 57 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THRBC 57 " --> pdb=" O METBC 3 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARGBC 5 " --> pdb=" O LEUBC 55 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEUBC 55 " --> pdb=" O ARGBC 5 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THRBC 7 " --> pdb=" O VALBC 53 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VALBC 53 " --> pdb=" O THRBC 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'BE' and resid 239 through 241 Processing sheet with id= E, first strand: chain 'BE' and resid 484 through 486 2072 hydrogen bonds defined for protein. 6177 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: 12.32 Time building geometry restraints manager: 16.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7228 1.33 - 1.45: 8780 1.45 - 1.57: 21461 1.57 - 1.70: 1 1.70 - 1.82: 347 Bond restraints: 37817 Sorted by residual: bond pdb=" C34 45DBH 400 " pdb=" C36 45DBH 400 " ideal model delta sigma weight residual 1.444 1.539 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C4A CYCAW 200 " pdb=" CHB CYCAW 200 " ideal model delta sigma weight residual 1.437 1.371 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C4A CYCAK 200 " pdb=" CHB CYCAK 200 " ideal model delta sigma weight residual 1.437 1.371 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C4A CYCAI 200 " pdb=" CHB CYCAI 200 " ideal model delta sigma weight residual 1.437 1.374 0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" C4A CYCAJ 200 " pdb=" CHB CYCAJ 200 " ideal model delta sigma weight residual 1.437 1.374 0.063 2.00e-02 2.50e+03 9.96e+00 ... (remaining 37812 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.76: 943 106.76 - 113.72: 19037 113.72 - 120.67: 17558 120.67 - 127.62: 13480 127.62 - 134.57: 239 Bond angle restraints: 51257 Sorted by residual: angle pdb=" N PHEBE 424 " pdb=" CA PHEBE 424 " pdb=" C PHEBE 424 " ideal model delta sigma weight residual 114.62 108.84 5.78 1.14e+00 7.69e-01 2.57e+01 angle pdb=" C SERAL 33 " pdb=" N GLYAL 34 " pdb=" CA GLYAL 34 " ideal model delta sigma weight residual 120.03 125.06 -5.03 1.12e+00 7.97e-01 2.02e+01 angle pdb=" C METAL 149 " pdb=" N GLYAL 150 " pdb=" CA GLYAL 150 " ideal model delta sigma weight residual 119.98 124.56 -4.58 1.11e+00 8.12e-01 1.70e+01 angle pdb=" C SERAK 33 " pdb=" N GLYAK 34 " pdb=" CA GLYAK 34 " ideal model delta sigma weight residual 119.98 124.55 -4.57 1.11e+00 8.12e-01 1.70e+01 angle pdb=" C ILEAC 157 " pdb=" N GLYAC 158 " pdb=" CA GLYAC 158 " ideal model delta sigma weight residual 119.98 124.48 -4.50 1.11e+00 8.12e-01 1.65e+01 ... (remaining 51252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 20072 17.44 - 34.88: 2569 34.88 - 52.33: 450 52.33 - 69.77: 265 69.77 - 87.21: 73 Dihedral angle restraints: 23429 sinusoidal: 9721 harmonic: 13708 Sorted by residual: dihedral pdb=" C THRBH 15 " pdb=" N THRBH 15 " pdb=" CA THRBH 15 " pdb=" CB THRBH 15 " ideal model delta harmonic sigma weight residual -122.00 -132.94 10.94 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C THRAW 102 " pdb=" N THRAW 102 " pdb=" CA THRAW 102 " pdb=" CB THRAW 102 " ideal model delta harmonic sigma weight residual -122.00 -132.47 10.47 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" C THRAN 102 " pdb=" N THRAN 102 " pdb=" CA THRAN 102 " pdb=" CB THRAN 102 " ideal model delta harmonic sigma weight residual -122.00 -132.11 10.11 0 2.50e+00 1.60e-01 1.63e+01 ... (remaining 23426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3369 0.067 - 0.135: 1823 0.135 - 0.202: 393 0.202 - 0.269: 138 0.269 - 0.337: 17 Chirality restraints: 5740 Sorted by residual: chirality pdb=" CA THRBH 15 " pdb=" N THRBH 15 " pdb=" C THRBH 15 " pdb=" CB THRBH 15 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA THRBE 528 " pdb=" N THRBE 528 " pdb=" C THRBE 528 " pdb=" CB THRBE 528 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA THRAW 102 " pdb=" N THRAW 102 " pdb=" C THRAW 102 " pdb=" CB THRAW 102 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 5737 not shown) Planarity restraints: 6586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CYCAX 200 " -0.076 2.00e-02 2.50e+03 2.70e-01 1.64e+03 pdb=" C2A CYCAX 200 " 0.115 2.00e-02 2.50e+03 pdb=" C3A CYCAX 200 " -0.113 2.00e-02 2.50e+03 pdb=" C4A CYCAX 200 " 0.079 2.00e-02 2.50e+03 pdb=" CAA CYCAX 200 " 0.470 2.00e-02 2.50e+03 pdb=" CHA CYCAX 200 " -0.304 2.00e-02 2.50e+03 pdb=" CHB CYCAX 200 " 0.297 2.00e-02 2.50e+03 pdb=" CMA CYCAX 200 " -0.466 2.00e-02 2.50e+03 pdb=" NA CYCAX 200 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAA 200 " 0.269 2.00e-02 2.50e+03 2.60e-01 1.52e+03 pdb=" OB CYCAA 200 " 0.072 2.00e-02 2.50e+03 pdb=" C1B CYCAA 200 " -0.039 2.00e-02 2.50e+03 pdb=" C2B CYCAA 200 " 0.120 2.00e-02 2.50e+03 pdb=" C3B CYCAA 200 " -0.068 2.00e-02 2.50e+03 pdb=" C4B CYCAA 200 " 0.093 2.00e-02 2.50e+03 pdb=" CAB CYCAA 200 " -0.392 2.00e-02 2.50e+03 pdb=" CHB CYCAA 200 " -0.444 2.00e-02 2.50e+03 pdb=" CMB CYCAA 200 " 0.390 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAY 200 " 0.290 2.00e-02 2.50e+03 2.41e-01 1.30e+03 pdb=" OB CYCAY 200 " 0.029 2.00e-02 2.50e+03 pdb=" C1B CYCAY 200 " -0.029 2.00e-02 2.50e+03 pdb=" C2B CYCAY 200 " 0.109 2.00e-02 2.50e+03 pdb=" C3B CYCAY 200 " -0.057 2.00e-02 2.50e+03 pdb=" C4B CYCAY 200 " 0.085 2.00e-02 2.50e+03 pdb=" CAB CYCAY 200 " -0.344 2.00e-02 2.50e+03 pdb=" CHB CYCAY 200 " -0.424 2.00e-02 2.50e+03 pdb=" CMB CYCAY 200 " 0.340 2.00e-02 2.50e+03 ... (remaining 6583 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 13971 2.95 - 3.44: 41718 3.44 - 3.93: 66871 3.93 - 4.41: 76139 4.41 - 4.90: 124789 Nonbonded interactions: 323488 Sorted by model distance: nonbonded pdb=" O ILEBE 192 " pdb=" OG1 THRBE 195 " model vdw 2.465 2.440 nonbonded pdb=" O ASNBG 241 " pdb=" OG SERBG 245 " model vdw 2.487 2.440 nonbonded pdb=" OG1 THRAW 5 " pdb=" OD2 ASPAX 3 " model vdw 2.509 2.440 nonbonded pdb=" O ARGBE 161 " pdb=" OG1 THRBE 164 " model vdw 2.532 2.440 nonbonded pdb=" O PHEBE 159 " pdb=" OG1 THRBE 163 " model vdw 2.551 2.440 ... (remaining 323483 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 'AH' selection = chain 'AJ' selection = chain 'AN' selection = chain 'AP' selection = chain 'AR' selection = chain 'AU' selection = chain 'AW' selection = chain 'AY' } ncs_group { reference = chain 'AB' selection = chain 'AD' selection = chain 'AF' selection = chain 'AI' selection = chain 'AL' selection = chain 'AO' selection = chain 'AQ' selection = chain 'AS' selection = chain 'AV' selection = chain 'AX' selection = chain 'AZ' } ncs_group { reference = chain 'BB' selection = chain 'BC' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.030 Extract box with map and model: 11.680 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 99.450 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 37817 Z= 0.481 Angle : 1.514 9.078 51257 Z= 1.025 Chirality : 0.085 0.337 5740 Planarity : 0.016 0.270 6586 Dihedral : 17.111 87.212 14695 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.57 % Favored : 96.22 % Rotamer: Outliers : 2.69 % Allowed : 9.39 % Favored : 87.92 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.74 (0.08), residues: 4683 helix: -3.07 (0.06), residues: 3608 sheet: -0.95 (0.73), residues: 46 loop : -2.43 (0.16), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPBE 158 HIS 0.002 0.001 HISAE 62 PHE 0.015 0.002 PHEBE 424 TYR 0.022 0.002 TYRBE 597 ARG 0.005 0.000 ARGAQ 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 878 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 6 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8652 (mtpt) REVERT: AA 10 ASN cc_start: 0.8892 (m110) cc_final: 0.8682 (m110) REVERT: AA 49 THR cc_start: 0.9178 (p) cc_final: 0.8967 (p) REVERT: AA 64 ASP cc_start: 0.9196 (p0) cc_final: 0.8961 (p0) REVERT: AA 105 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7720 (mm-30) REVERT: AA 128 GLN cc_start: 0.8466 (tp-100) cc_final: 0.8190 (tp40) REVERT: AB 10 ASN cc_start: 0.8834 (t0) cc_final: 0.8392 (t0) REVERT: AB 13 ASP cc_start: 0.8477 (t70) cc_final: 0.8086 (t0) REVERT: AB 100 ASP cc_start: 0.7911 (t70) cc_final: 0.7662 (t0) REVERT: AB 157 CYS cc_start: 0.8703 (m) cc_final: 0.8297 (m) REVERT: AC 24 ASP cc_start: 0.8198 (m-30) cc_final: 0.7694 (t0) REVERT: AC 27 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8653 (tmmt) REVERT: AC 52 LYS cc_start: 0.8801 (tptp) cc_final: 0.8129 (tppt) REVERT: AC 60 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8388 (tm-30) REVERT: AC 61 LYS cc_start: 0.9160 (ttmm) cc_final: 0.8865 (ttmm) REVERT: AC 124 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: AC 141 MET cc_start: 0.7582 (ptp) cc_final: 0.7173 (ptt) REVERT: AD 2 GLN cc_start: 0.8112 (pm20) cc_final: 0.7729 (pm20) REVERT: AD 37 ARG cc_start: 0.9043 (mtt90) cc_final: 0.8731 (mtp85) REVERT: AD 71 ASN cc_start: 0.6685 (t0) cc_final: 0.6253 (t0) REVERT: AD 117 ASN cc_start: 0.9052 (m110) cc_final: 0.8851 (m-40) REVERT: AD 131 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7369 (tm-30) REVERT: AE 14 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8715 (mp10) REVERT: AE 37 ILE cc_start: 0.8908 (mt) cc_final: 0.8697 (mm) REVERT: AE 60 LYS cc_start: 0.9199 (ttpp) cc_final: 0.8908 (tmmm) REVERT: AE 128 ASP cc_start: 0.8701 (m-30) cc_final: 0.8445 (m-30) REVERT: AF 17 LYS cc_start: 0.7739 (mtmp) cc_final: 0.7518 (mtmm) REVERT: AF 71 ASN cc_start: 0.8580 (t0) cc_final: 0.8308 (t0) REVERT: AF 86 ASP cc_start: 0.7771 (t70) cc_final: 0.7513 (t0) REVERT: AF 100 ASP cc_start: 0.7632 (t70) cc_final: 0.7285 (t0) REVERT: AF 131 GLN cc_start: 0.8232 (mm110) cc_final: 0.7893 (mm-40) REVERT: AI 2 GLN cc_start: 0.7764 (mt0) cc_final: 0.7520 (mt0) REVERT: AJ 52 LYS cc_start: 0.8404 (tmtm) cc_final: 0.7995 (tptp) REVERT: AJ 141 MET cc_start: 0.7852 (ptp) cc_final: 0.7595 (ptp) REVERT: AN 91 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8375 (mm) REVERT: AO 96 MET cc_start: 0.8172 (tmm) cc_final: 0.7919 (tmm) REVERT: AU 53 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7629 (tm-30) REVERT: AU 145 ASP cc_start: 0.8477 (m-30) cc_final: 0.7983 (m-30) REVERT: AV 15 GLN cc_start: 0.8148 (mp10) cc_final: 0.7869 (mp10) REVERT: AW 88 TYR cc_start: 0.8085 (m-80) cc_final: 0.7881 (m-80) REVERT: AW 144 ASP cc_start: 0.7665 (p0) cc_final: 0.7416 (p0) REVERT: AW 160 MET cc_start: 0.8682 (tpp) cc_final: 0.8465 (mmt) REVERT: BB 24 ASN cc_start: 0.8223 (t0) cc_final: 0.7747 (t0) REVERT: BB 46 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5915 (mmt) REVERT: BB 53 VAL cc_start: 0.8285 (m) cc_final: 0.8050 (t) REVERT: BH 32 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8294 (p0) REVERT: BH 164 THR cc_start: 0.8607 (p) cc_final: 0.8321 (t) REVERT: BH 174 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.5717 (pp20) outliers start: 102 outliers final: 13 residues processed: 945 average time/residue: 1.5819 time to fit residues: 1782.6142 Evaluate side-chains 609 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 590 time to evaluate : 7.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 128 GLN Chi-restraints excluded: chain AC residue 96 VAL Chi-restraints excluded: chain AC residue 124 GLU Chi-restraints excluded: chain AE residue 14 GLN Chi-restraints excluded: chain AE residue 149 THR Chi-restraints excluded: chain AJ residue 9 VAL Chi-restraints excluded: chain AJ residue 66 VAL Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 144 ASP Chi-restraints excluded: chain AN residue 91 LEU Chi-restraints excluded: chain AU residue 30 VAL Chi-restraints excluded: chain AV residue 112 LEU Chi-restraints excluded: chain BB residue 46 MET Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BH residue 32 ASN Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 6.9990 chunk 354 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 366 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 424 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 53 GLN AA 128 GLN AB 131 GLN AD 71 ASN AE 79 ASN AE 117 ASN AE 120 ASN AF 15 GLN AF 71 ASN AH 10 ASN AK 22 ASN AK 72 ASN AO 10 ASN AO 71 ASN AQ 71 ASN ** AS 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 10 ASN AX 2 GLN AZ 71 ASN BB 40 GLN BE 27 GLN BE 30 GLN BE 213 ASN BE 451 ASN ** BH 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 97 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37817 Z= 0.260 Angle : 0.634 11.439 51257 Z= 0.311 Chirality : 0.037 0.182 5740 Planarity : 0.004 0.034 6586 Dihedral : 8.511 89.460 6424 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.75 % Favored : 98.23 % Rotamer: Outliers : 3.30 % Allowed : 18.49 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.11), residues: 4683 helix: -0.24 (0.08), residues: 3628 sheet: -0.26 (0.73), residues: 44 loop : -1.61 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPBE 158 HIS 0.002 0.001 HISAK 159 PHE 0.015 0.002 PHEBE 624 TYR 0.021 0.002 TYRBE 597 ARG 0.008 0.001 ARGBE 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 619 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 42 THR cc_start: 0.8801 (m) cc_final: 0.8511 (p) REVERT: AA 64 ASP cc_start: 0.9327 (p0) cc_final: 0.9024 (p0) REVERT: AA 105 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7871 (mm-30) REVERT: AA 128 GLN cc_start: 0.8551 (tp40) cc_final: 0.8313 (tp40) REVERT: AA 138 SER cc_start: 0.8910 (m) cc_final: 0.8565 (p) REVERT: AB 13 ASP cc_start: 0.8603 (t70) cc_final: 0.8387 (t0) REVERT: AB 28 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8776 (mmmm) REVERT: AB 35 GLU cc_start: 0.8262 (mp0) cc_final: 0.7923 (mp0) REVERT: AB 100 ASP cc_start: 0.7905 (t70) cc_final: 0.7269 (t0) REVERT: AB 113 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8259 (tptm) REVERT: AB 117 ASN cc_start: 0.8590 (m-40) cc_final: 0.8273 (m-40) REVERT: AC 24 ASP cc_start: 0.8420 (m-30) cc_final: 0.8052 (t0) REVERT: AC 27 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8671 (tmmt) REVERT: AC 52 LYS cc_start: 0.8920 (tptp) cc_final: 0.8626 (tppt) REVERT: AC 60 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8409 (tm-30) REVERT: AC 61 LYS cc_start: 0.9116 (ttmm) cc_final: 0.8765 (ttmm) REVERT: AD 2 GLN cc_start: 0.8124 (pm20) cc_final: 0.7817 (pm20) REVERT: AD 37 ARG cc_start: 0.9082 (mtt90) cc_final: 0.8768 (mtp85) REVERT: AD 128 GLN cc_start: 0.8106 (tp40) cc_final: 0.7705 (mm110) REVERT: AD 131 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7341 (tm-30) REVERT: AD 135 GLU cc_start: 0.8517 (mp0) cc_final: 0.7919 (mp0) REVERT: AE 47 GLU cc_start: 0.7915 (tp30) cc_final: 0.7679 (tp30) REVERT: AE 60 LYS cc_start: 0.9148 (ttpp) cc_final: 0.8709 (tptp) REVERT: AE 61 LYS cc_start: 0.9035 (tttp) cc_final: 0.8740 (tttt) REVERT: AF 100 ASP cc_start: 0.7589 (t70) cc_final: 0.7262 (t0) REVERT: AK 141 MET cc_start: 0.7414 (ttm) cc_final: 0.7141 (ttm) REVERT: AU 6 LYS cc_start: 0.9131 (mttp) cc_final: 0.8879 (mttt) REVERT: AU 27 LYS cc_start: 0.9045 (ptmm) cc_final: 0.8775 (ptpp) REVERT: AU 53 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7729 (tm-30) REVERT: AU 100 ASP cc_start: 0.7924 (t0) cc_final: 0.7657 (t0) REVERT: AU 144 ASP cc_start: 0.7138 (p0) cc_final: 0.6908 (p0) REVERT: AV 15 GLN cc_start: 0.8351 (mp10) cc_final: 0.8004 (mp10) REVERT: AV 106 GLU cc_start: 0.7919 (tt0) cc_final: 0.7718 (tt0) REVERT: AV 147 LYS cc_start: 0.9006 (tppp) cc_final: 0.8624 (tppt) REVERT: AW 160 MET cc_start: 0.8585 (tpp) cc_final: 0.8319 (mmt) REVERT: AY 160 MET cc_start: 0.9127 (tpp) cc_final: 0.8841 (mmt) REVERT: AZ 15 GLN cc_start: 0.8701 (mp10) cc_final: 0.8395 (mp10) REVERT: BB 24 ASN cc_start: 0.8485 (t0) cc_final: 0.8001 (t0) REVERT: BE 255 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: BH 32 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.7745 (p0) REVERT: BH 174 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6698 (pp20) REVERT: BI 116 GLN cc_start: 0.8109 (mm110) cc_final: 0.7857 (mm110) outliers start: 125 outliers final: 38 residues processed: 697 average time/residue: 1.6323 time to fit residues: 1356.0775 Evaluate side-chains 585 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 543 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 5 THR Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 113 LYS Chi-restraints excluded: chain AB residue 156 ILE Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 64 ASP Chi-restraints excluded: chain AF residue 137 THR Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 102 THR Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 160 MET Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AP residue 100 ASP Chi-restraints excluded: chain AS residue 26 LYS Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AU residue 5 THR Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 89 LEU Chi-restraints excluded: chain AX residue 27 LEU Chi-restraints excluded: chain BB residue 14 THR Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 255 GLN Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 32 ASN Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 174 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 236 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 353 optimal weight: 0.9990 chunk 289 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 425 optimal weight: 5.9990 chunk 459 optimal weight: 0.9990 chunk 379 optimal weight: 10.0000 chunk 422 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AE 10 GLN AE 77 GLN AE 120 ASN AF 71 ASN AI 2 GLN ** AS 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 131 GLN AV 2 GLN BC 13 GLN ** BH 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 97 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37817 Z= 0.169 Angle : 0.568 11.067 51257 Z= 0.273 Chirality : 0.036 0.162 5740 Planarity : 0.003 0.056 6586 Dihedral : 8.034 87.710 6400 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.03 % Favored : 97.95 % Rotamer: Outliers : 2.72 % Allowed : 19.59 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.12), residues: 4683 helix: 0.88 (0.08), residues: 3599 sheet: -0.02 (0.73), residues: 44 loop : -1.26 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPBE 158 HIS 0.002 0.001 HISAK 159 PHE 0.014 0.001 PHEBE 76 TYR 0.019 0.001 TYRBE 597 ARG 0.012 0.000 ARGAD 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 586 time to evaluate : 4.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 42 THR cc_start: 0.8826 (m) cc_final: 0.8565 (p) REVERT: AA 64 ASP cc_start: 0.9331 (p0) cc_final: 0.9007 (p0) REVERT: AA 105 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7828 (mm-30) REVERT: AA 138 SER cc_start: 0.8922 (m) cc_final: 0.8575 (p) REVERT: AB 28 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8729 (mmmm) REVERT: AB 35 GLU cc_start: 0.8253 (mp0) cc_final: 0.7949 (mp0) REVERT: AB 67 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7503 (mtm110) REVERT: AB 100 ASP cc_start: 0.7890 (t70) cc_final: 0.7239 (t0) REVERT: AC 24 ASP cc_start: 0.8407 (m-30) cc_final: 0.8036 (t0) REVERT: AC 52 LYS cc_start: 0.8862 (tptp) cc_final: 0.8628 (tppt) REVERT: AC 53 GLN cc_start: 0.8324 (mp10) cc_final: 0.8043 (mp10) REVERT: AC 60 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8484 (tm-30) REVERT: AC 61 LYS cc_start: 0.9116 (ttmm) cc_final: 0.8872 (ttmt) REVERT: AC 159 LYS cc_start: 0.9382 (ttmm) cc_final: 0.9061 (tppp) REVERT: AD 2 GLN cc_start: 0.8155 (pm20) cc_final: 0.7771 (pm20) REVERT: AD 39 ARG cc_start: 0.8806 (mmm160) cc_final: 0.8587 (mmm160) REVERT: AD 128 GLN cc_start: 0.8051 (tp40) cc_final: 0.7817 (mm110) REVERT: AD 131 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7396 (tm-30) REVERT: AD 135 GLU cc_start: 0.8487 (mp0) cc_final: 0.7721 (mp0) REVERT: AE 60 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8700 (tptp) REVERT: AE 61 LYS cc_start: 0.9067 (tttp) cc_final: 0.8808 (tttt) REVERT: AF 15 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: AF 17 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7608 (mtmm) REVERT: AF 100 ASP cc_start: 0.7592 (t70) cc_final: 0.7253 (t0) REVERT: AF 114 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8321 (tt0) REVERT: AK 141 MET cc_start: 0.7440 (ttm) cc_final: 0.7207 (ttm) REVERT: AN 115 MET cc_start: 0.8551 (tmm) cc_final: 0.8292 (tmm) REVERT: AO 24 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8078 (mmm) REVERT: AQ 149 MET cc_start: 0.8767 (mmm) cc_final: 0.8392 (tpp) REVERT: AU 6 LYS cc_start: 0.9128 (mttp) cc_final: 0.8909 (mttt) REVERT: AU 27 LYS cc_start: 0.9010 (ptmm) cc_final: 0.8751 (ptpp) REVERT: AU 144 ASP cc_start: 0.7250 (p0) cc_final: 0.6866 (p0) REVERT: AU 145 ASP cc_start: 0.8236 (m-30) cc_final: 0.7836 (m-30) REVERT: AV 15 GLN cc_start: 0.8419 (mp10) cc_final: 0.8079 (mp10) REVERT: AV 26 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9052 (mmmm) REVERT: AV 35 GLU cc_start: 0.7927 (tp30) cc_final: 0.7540 (tp30) REVERT: AV 39 ARG cc_start: 0.8462 (ptp-110) cc_final: 0.8200 (ptp-110) REVERT: AV 147 LYS cc_start: 0.8959 (tppp) cc_final: 0.8602 (tppt) REVERT: AW 160 MET cc_start: 0.8540 (tpp) cc_final: 0.8262 (mmt) REVERT: AZ 15 GLN cc_start: 0.8744 (mp10) cc_final: 0.8470 (mp10) REVERT: BB 5 ARG cc_start: 0.8507 (tpp80) cc_final: 0.8304 (tpp80) REVERT: BB 24 ASN cc_start: 0.8491 (t0) cc_final: 0.8011 (t0) REVERT: BH 34 GLU cc_start: 0.7822 (pm20) cc_final: 0.7185 (pm20) REVERT: BH 74 MET cc_start: 0.7989 (mtp) cc_final: 0.7782 (mtp) REVERT: BH 174 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6755 (pp20) outliers start: 103 outliers final: 38 residues processed: 653 average time/residue: 1.5981 time to fit residues: 1244.3424 Evaluate side-chains 577 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 534 time to evaluate : 4.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 LEU Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 67 ARG Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AJ residue 66 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AO residue 24 MET Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AS residue 26 LYS Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AU residue 89 LEU Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 26 LYS Chi-restraints excluded: chain AW residue 145 ASP Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Chi-restraints excluded: chain BI residue 97 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 420 optimal weight: 0.6980 chunk 320 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 285 optimal weight: 8.9990 chunk 427 optimal weight: 10.0000 chunk 452 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 404 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AE 77 GLN AE 120 ASN AF 71 ASN AV 2 GLN ** BH 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37817 Z= 0.166 Angle : 0.556 12.249 51257 Z= 0.267 Chirality : 0.035 0.168 5740 Planarity : 0.003 0.038 6586 Dihedral : 7.901 87.176 6398 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.73 % Favored : 98.25 % Rotamer: Outliers : 2.82 % Allowed : 20.52 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.12), residues: 4683 helix: 1.37 (0.09), residues: 3577 sheet: -0.32 (0.82), residues: 38 loop : -1.09 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBE 158 HIS 0.001 0.000 HISAK 159 PHE 0.014 0.001 PHEBE 76 TYR 0.019 0.001 TYRBE 597 ARG 0.007 0.000 ARGBB 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 579 time to evaluate : 4.603 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: AA 42 THR cc_start: 0.8894 (m) cc_final: 0.8657 (p) REVERT: AA 64 ASP cc_start: 0.9326 (p0) cc_final: 0.9000 (p0) REVERT: AA 105 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7819 (mm-30) REVERT: AA 138 SER cc_start: 0.8968 (m) cc_final: 0.8584 (p) REVERT: AB 28 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8716 (mmmm) REVERT: AB 35 GLU cc_start: 0.8210 (mp0) cc_final: 0.7929 (mp0) REVERT: AB 54 GLU cc_start: 0.8382 (tp30) cc_final: 0.8175 (tp30) REVERT: AB 67 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7358 (mtm110) REVERT: AB 117 ASN cc_start: 0.8544 (m-40) cc_final: 0.8343 (m-40) REVERT: AC 52 LYS cc_start: 0.8850 (tptp) cc_final: 0.8527 (tppt) REVERT: AC 60 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8509 (tm-30) REVERT: AC 61 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8873 (ttmt) REVERT: AC 159 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9036 (tppp) REVERT: AD 2 GLN cc_start: 0.8100 (pm20) cc_final: 0.7766 (pm20) REVERT: AD 128 GLN cc_start: 0.8045 (tp40) cc_final: 0.7819 (mm110) REVERT: AD 131 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7145 (tm-30) REVERT: AD 135 GLU cc_start: 0.8514 (mp0) cc_final: 0.7596 (mp0) REVERT: AD 154 ASP cc_start: 0.8751 (m-30) cc_final: 0.8541 (m-30) REVERT: AE 56 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8277 (tmmt) REVERT: AE 61 LYS cc_start: 0.9076 (tttp) cc_final: 0.8813 (tttt) REVERT: AE 89 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8772 (tp) REVERT: AE 105 GLU cc_start: 0.7876 (tp30) cc_final: 0.7325 (tp30) REVERT: AE 126 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8744 (ttt) REVERT: AF 15 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: AF 100 ASP cc_start: 0.7639 (t70) cc_final: 0.7283 (t0) REVERT: AK 24 MET cc_start: 0.7933 (mmt) cc_final: 0.7458 (mmt) REVERT: AK 141 MET cc_start: 0.7438 (ttm) cc_final: 0.7222 (ttm) REVERT: AQ 149 MET cc_start: 0.8748 (mmm) cc_final: 0.8500 (tpp) REVERT: AU 27 LYS cc_start: 0.9047 (ptmm) cc_final: 0.8796 (ptpp) REVERT: AU 115 MET cc_start: 0.8348 (tmm) cc_final: 0.8099 (tmt) REVERT: AU 144 ASP cc_start: 0.7266 (p0) cc_final: 0.6861 (p0) REVERT: AU 145 ASP cc_start: 0.8252 (m-30) cc_final: 0.7776 (m-30) REVERT: AU 152 TYR cc_start: 0.7620 (m-80) cc_final: 0.7417 (m-80) REVERT: AV 1 MET cc_start: 0.7666 (pmm) cc_final: 0.7313 (ppp) REVERT: AV 15 GLN cc_start: 0.8504 (mp10) cc_final: 0.8093 (mp10) REVERT: AV 26 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.9049 (mmmm) REVERT: AV 35 GLU cc_start: 0.8034 (tp30) cc_final: 0.7595 (tp30) REVERT: AV 39 ARG cc_start: 0.8472 (ptp-110) cc_final: 0.8154 (ptp-110) REVERT: AV 147 LYS cc_start: 0.8920 (tppp) cc_final: 0.8554 (tppt) REVERT: AV 149 MET cc_start: 0.8969 (tpp) cc_final: 0.8721 (tpt) REVERT: AW 160 MET cc_start: 0.8484 (tpp) cc_final: 0.8214 (mmt) REVERT: BB 24 ASN cc_start: 0.8504 (t0) cc_final: 0.8025 (t0) REVERT: BB 46 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6881 (mpt) REVERT: BE 255 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: BH 174 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6741 (pp20) REVERT: BI 113 MET cc_start: 0.7991 (mtm) cc_final: 0.7692 (mtm) outliers start: 107 outliers final: 45 residues processed: 651 average time/residue: 1.6128 time to fit residues: 1254.2349 Evaluate side-chains 598 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 544 time to evaluate : 4.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 LEU Chi-restraints excluded: chain AB residue 67 ARG Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AC residue 159 LYS Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AE residue 9 LEU Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AE residue 89 LEU Chi-restraints excluded: chain AE residue 126 MET Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 113 LEU Chi-restraints excluded: chain AK residue 151 ASP Chi-restraints excluded: chain AL residue 161 SER Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 141 VAL Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 53 GLN Chi-restraints excluded: chain AU residue 89 LEU Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 26 LYS Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AW residue 145 ASP Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 46 MET Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 255 GLN Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 240 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 71 ILE Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 376 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 336 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 386 optimal weight: 6.9990 chunk 312 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 406 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 53 GLN ** AD 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AF 2 GLN AF 15 GLN AF 71 ASN AF 128 GLN AR 60 GLN AV 2 GLN BC 13 GLN BE 444 GLN BE 451 ASN ** BH 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 97 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 37817 Z= 0.363 Angle : 0.660 11.900 51257 Z= 0.321 Chirality : 0.040 0.181 5740 Planarity : 0.004 0.086 6586 Dihedral : 7.682 85.898 6398 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 3.77 % Allowed : 20.15 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.12), residues: 4683 helix: 1.47 (0.09), residues: 3596 sheet: 0.73 (0.90), residues: 32 loop : -0.90 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPBE 158 HIS 0.003 0.001 HISBE 349 PHE 0.018 0.002 PHEBE 76 TYR 0.028 0.002 TYRBE 597 ARG 0.015 0.001 ARGAD 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 570 time to evaluate : 4.370 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: AA 42 THR cc_start: 0.8850 (m) cc_final: 0.8535 (p) REVERT: AA 64 ASP cc_start: 0.9370 (p0) cc_final: 0.9025 (p0) REVERT: AA 105 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7861 (mm-30) REVERT: AA 138 SER cc_start: 0.9078 (m) cc_final: 0.8840 (p) REVERT: AB 28 LYS cc_start: 0.9185 (mmtt) cc_final: 0.8797 (mmmm) REVERT: AB 35 GLU cc_start: 0.8277 (mp0) cc_final: 0.8002 (mp0) REVERT: AB 53 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8553 (tmtm) REVERT: AB 113 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8124 (tptm) REVERT: AB 117 ASN cc_start: 0.8544 (m-40) cc_final: 0.8159 (m-40) REVERT: AC 53 GLN cc_start: 0.8808 (mt0) cc_final: 0.8226 (mp10) REVERT: AC 60 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8525 (tm-30) REVERT: AC 61 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8800 (ttmt) REVERT: AC 159 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9049 (tppp) REVERT: AD 2 GLN cc_start: 0.8165 (pm20) cc_final: 0.7903 (pm20) REVERT: AD 17 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8754 (ptpp) REVERT: AD 128 GLN cc_start: 0.8120 (tp40) cc_final: 0.7898 (mm110) REVERT: AD 131 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7404 (tm-30) REVERT: AD 135 GLU cc_start: 0.8562 (mp0) cc_final: 0.7901 (mp0) REVERT: AD 154 ASP cc_start: 0.8771 (m-30) cc_final: 0.8535 (m-30) REVERT: AE 56 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8388 (pptt) REVERT: AE 60 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8890 (tmmm) REVERT: AE 61 LYS cc_start: 0.9236 (tttp) cc_final: 0.8994 (tttt) REVERT: AE 105 GLU cc_start: 0.7860 (tp30) cc_final: 0.7328 (tp30) REVERT: AF 2 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: AF 15 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7879 (mp-120) REVERT: AF 71 ASN cc_start: 0.8543 (t160) cc_final: 0.8305 (t0) REVERT: AF 100 ASP cc_start: 0.7746 (t70) cc_final: 0.7438 (t0) REVERT: AH 161 SER cc_start: 0.7472 (OUTLIER) cc_final: 0.7176 (p) REVERT: AK 141 MET cc_start: 0.7561 (ttm) cc_final: 0.7307 (ttm) REVERT: AO 28 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8327 (mtmm) REVERT: AQ 149 MET cc_start: 0.8797 (mmm) cc_final: 0.8393 (tpp) REVERT: AU 27 LYS cc_start: 0.9084 (ptmm) cc_final: 0.8814 (ptpp) REVERT: AU 144 ASP cc_start: 0.7326 (p0) cc_final: 0.7051 (p0) REVERT: AU 152 TYR cc_start: 0.7990 (m-80) cc_final: 0.7775 (m-80) REVERT: AV 15 GLN cc_start: 0.8512 (mp10) cc_final: 0.8177 (mp10) REVERT: AV 35 GLU cc_start: 0.8072 (tp30) cc_final: 0.7660 (tp30) REVERT: AV 39 ARG cc_start: 0.8506 (ptp-110) cc_final: 0.8208 (ptp-110) REVERT: AV 147 LYS cc_start: 0.8999 (tppp) cc_final: 0.8653 (tppt) REVERT: BB 5 ARG cc_start: 0.8546 (tpp80) cc_final: 0.8321 (tpp80) REVERT: BB 24 ASN cc_start: 0.8633 (t0) cc_final: 0.8274 (t0) REVERT: BB 46 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7105 (mpt) REVERT: BH 174 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7110 (pp20) outliers start: 143 outliers final: 64 residues processed: 652 average time/residue: 1.6229 time to fit residues: 1267.7070 Evaluate side-chains 610 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 538 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 49 THR Chi-restraints excluded: chain AA residue 89 LEU Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 53 LYS Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 105 ASP Chi-restraints excluded: chain AB residue 113 LYS Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AC residue 159 LYS Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AD residue 161 SER Chi-restraints excluded: chain AE residue 85 TYR Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AE residue 145 ASP Chi-restraints excluded: chain AF residue 2 GLN Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 15 GLN Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 24 MET Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 64 ASP Chi-restraints excluded: chain AF residue 123 ILE Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AF residue 161 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 52 LYS Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AH residue 161 SER Chi-restraints excluded: chain AI residue 36 LEU Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AJ residue 97 VAL Chi-restraints excluded: chain AK residue 61 GLU Chi-restraints excluded: chain AK residue 97 LEU Chi-restraints excluded: chain AK residue 105 LEU Chi-restraints excluded: chain AK residue 151 ASP Chi-restraints excluded: chain AK residue 160 MET Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 161 SER Chi-restraints excluded: chain AN residue 37 LEU Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AO residue 100 ASP Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 141 VAL Chi-restraints excluded: chain AU residue 5 THR Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 89 LEU Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AW residue 65 ILE Chi-restraints excluded: chain AW residue 145 ASP Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 14 THR Chi-restraints excluded: chain BB residue 46 MET Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 212 ASN Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Chi-restraints excluded: chain BI residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 152 optimal weight: 0.8980 chunk 407 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 452 optimal weight: 5.9990 chunk 375 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 237 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AR 60 GLN AY 128 GLN BB 13 GLN BI 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37817 Z= 0.191 Angle : 0.595 12.368 51257 Z= 0.285 Chirality : 0.036 0.183 5740 Planarity : 0.003 0.049 6586 Dihedral : 7.720 88.753 6398 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.21 % Rotamer: Outliers : 3.14 % Allowed : 21.28 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.12), residues: 4683 helix: 1.64 (0.09), residues: 3598 sheet: 0.46 (1.07), residues: 26 loop : -0.78 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPBE 158 HIS 0.001 0.001 HISBE 349 PHE 0.011 0.001 PHEBE 424 TYR 0.021 0.001 TYRBE 597 ARG 0.013 0.000 ARGAD 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 562 time to evaluate : 4.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 42 THR cc_start: 0.8910 (m) cc_final: 0.8646 (p) REVERT: AA 64 ASP cc_start: 0.9356 (p0) cc_final: 0.9005 (p0) REVERT: AA 105 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7817 (mm-30) REVERT: AA 138 SER cc_start: 0.9069 (m) cc_final: 0.8822 (p) REVERT: AB 28 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8789 (mmmm) REVERT: AB 35 GLU cc_start: 0.8262 (mp0) cc_final: 0.8023 (mp0) REVERT: AB 53 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8507 (tmtm) REVERT: AB 67 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7636 (mtm180) REVERT: AC 60 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8548 (tm-30) REVERT: AC 61 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8830 (ttmt) REVERT: AD 17 LYS cc_start: 0.8914 (ptpp) cc_final: 0.8664 (ptpp) REVERT: AD 131 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7322 (tm-30) REVERT: AD 135 GLU cc_start: 0.8557 (mp0) cc_final: 0.7849 (mp0) REVERT: AD 154 ASP cc_start: 0.8735 (m-30) cc_final: 0.8515 (m-30) REVERT: AE 32 THR cc_start: 0.8659 (p) cc_final: 0.8271 (t) REVERT: AE 49 LYS cc_start: 0.8671 (tptp) cc_final: 0.8362 (tptp) REVERT: AE 60 LYS cc_start: 0.9093 (ttpp) cc_final: 0.8876 (tmmm) REVERT: AE 105 GLU cc_start: 0.7839 (tp30) cc_final: 0.7248 (tp30) REVERT: AF 72 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8728 (ttt) REVERT: AF 100 ASP cc_start: 0.7737 (t70) cc_final: 0.7354 (t0) REVERT: AK 141 MET cc_start: 0.7499 (ttm) cc_final: 0.7203 (ttm) REVERT: AO 28 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8265 (mtmm) REVERT: AQ 149 MET cc_start: 0.8748 (mmm) cc_final: 0.8515 (tpp) REVERT: AU 6 LYS cc_start: 0.9050 (mmtp) cc_final: 0.8814 (mttp) REVERT: AU 27 LYS cc_start: 0.9084 (ptmm) cc_final: 0.8810 (ptpp) REVERT: AU 100 ASP cc_start: 0.8183 (t0) cc_final: 0.7856 (t0) REVERT: AU 144 ASP cc_start: 0.7363 (p0) cc_final: 0.7084 (p0) REVERT: AU 152 TYR cc_start: 0.7834 (m-80) cc_final: 0.7605 (m-80) REVERT: AV 1 MET cc_start: 0.7508 (pmm) cc_final: 0.7192 (ppp) REVERT: AV 15 GLN cc_start: 0.8454 (mp10) cc_final: 0.8210 (mp10) REVERT: AV 147 LYS cc_start: 0.9038 (tppp) cc_final: 0.8624 (tppt) REVERT: BB 24 ASN cc_start: 0.8592 (t0) cc_final: 0.8211 (t0) REVERT: BB 44 MET cc_start: 0.8997 (ptm) cc_final: 0.8793 (ptm) REVERT: BC 44 MET cc_start: 0.7947 (mtt) cc_final: 0.7272 (mtt) REVERT: BH 174 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6709 (pp20) outliers start: 119 outliers final: 50 residues processed: 639 average time/residue: 1.5755 time to fit residues: 1208.0803 Evaluate side-chains 589 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 536 time to evaluate : 4.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 LEU Chi-restraints excluded: chain AB residue 67 ARG Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 71 ASN Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 24 MET Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 72 MET Chi-restraints excluded: chain AF residue 137 THR Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 151 ASP Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 19 LEU Chi-restraints excluded: chain AL residue 161 SER Chi-restraints excluded: chain AN residue 37 LEU Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AO residue 100 ASP Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 141 VAL Chi-restraints excluded: chain AS residue 144 ASP Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 89 LEU Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AW residue 145 ASP Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 14 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 174 GLU Chi-restraints excluded: chain BI residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 436 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 330 optimal weight: 7.9990 chunk 256 optimal weight: 9.9990 chunk 381 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 451 optimal weight: 0.9990 chunk 282 optimal weight: 0.7980 chunk 275 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN BC 13 GLN BI 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37817 Z= 0.219 Angle : 0.610 11.811 51257 Z= 0.293 Chirality : 0.037 0.182 5740 Planarity : 0.004 0.085 6586 Dihedral : 7.618 87.879 6393 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 2.93 % Allowed : 22.13 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.12), residues: 4683 helix: 1.69 (0.09), residues: 3608 sheet: 0.46 (1.08), residues: 26 loop : -0.69 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBE 158 HIS 0.002 0.001 HISBE 349 PHE 0.012 0.001 PHEBE 424 TYR 0.026 0.001 TYRAY 88 ARG 0.016 0.000 ARGAD 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 553 time to evaluate : 4.586 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: AA 42 THR cc_start: 0.8997 (m) cc_final: 0.8734 (p) REVERT: AA 64 ASP cc_start: 0.9360 (p0) cc_final: 0.9034 (p0) REVERT: AA 105 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7824 (mm-30) REVERT: AA 138 SER cc_start: 0.9071 (m) cc_final: 0.8831 (p) REVERT: AB 28 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8787 (mmmm) REVERT: AB 35 GLU cc_start: 0.8264 (mp0) cc_final: 0.8013 (mp0) REVERT: AB 53 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8626 (tmtm) REVERT: AB 54 GLU cc_start: 0.8333 (tp30) cc_final: 0.8121 (tp30) REVERT: AC 53 GLN cc_start: 0.8743 (mt0) cc_final: 0.8367 (mp10) REVERT: AC 60 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8552 (tm-30) REVERT: AC 61 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8831 (ttmt) REVERT: AC 141 MET cc_start: 0.7186 (pp-130) cc_final: 0.6745 (pp-130) REVERT: AD 2 GLN cc_start: 0.8219 (pm20) cc_final: 0.7860 (pm20) REVERT: AD 17 LYS cc_start: 0.8842 (ptpp) cc_final: 0.8543 (ptpp) REVERT: AE 32 THR cc_start: 0.8594 (p) cc_final: 0.8214 (t) REVERT: AE 49 LYS cc_start: 0.8687 (tptp) cc_final: 0.8217 (tptp) REVERT: AE 60 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8852 (tmmm) REVERT: AE 105 GLU cc_start: 0.7814 (tp30) cc_final: 0.7256 (tp30) REVERT: AE 126 MET cc_start: 0.9198 (mtp) cc_final: 0.8997 (ttt) REVERT: AF 72 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8723 (ttt) REVERT: AF 100 ASP cc_start: 0.7690 (t70) cc_final: 0.7322 (t0) REVERT: AK 141 MET cc_start: 0.7518 (ttm) cc_final: 0.7211 (ttm) REVERT: AO 28 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8303 (mtmm) REVERT: AQ 149 MET cc_start: 0.8754 (mmm) cc_final: 0.8519 (tpp) REVERT: AU 6 LYS cc_start: 0.9033 (mmtp) cc_final: 0.8777 (mttp) REVERT: AU 27 LYS cc_start: 0.9121 (ptmm) cc_final: 0.8879 (ptpp) REVERT: AU 100 ASP cc_start: 0.8178 (t0) cc_final: 0.7852 (t0) REVERT: AU 144 ASP cc_start: 0.7388 (p0) cc_final: 0.6829 (p0) REVERT: AU 145 ASP cc_start: 0.8404 (m-30) cc_final: 0.7814 (m-30) REVERT: AU 152 TYR cc_start: 0.7792 (m-80) cc_final: 0.7547 (m-80) REVERT: AV 1 MET cc_start: 0.7480 (pmm) cc_final: 0.7202 (ppp) REVERT: AV 15 GLN cc_start: 0.8472 (mp10) cc_final: 0.8127 (mp10) REVERT: AV 147 LYS cc_start: 0.9047 (tppp) cc_final: 0.8628 (tppt) REVERT: AW 52 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8705 (ttpp) REVERT: BB 24 ASN cc_start: 0.8590 (t0) cc_final: 0.8228 (t0) REVERT: BC 44 MET cc_start: 0.7981 (mtt) cc_final: 0.7316 (mtt) outliers start: 111 outliers final: 58 residues processed: 618 average time/residue: 1.6015 time to fit residues: 1182.5666 Evaluate side-chains 593 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 533 time to evaluate : 4.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 49 THR Chi-restraints excluded: chain AA residue 89 LEU Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 53 LYS Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 5 THR Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AE residue 149 THR Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 72 MET Chi-restraints excluded: chain AF residue 137 THR Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 49 THR Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 105 LEU Chi-restraints excluded: chain AK residue 151 ASP Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 19 LEU Chi-restraints excluded: chain AL residue 161 SER Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AO residue 100 ASP Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AS residue 144 ASP Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 89 LEU Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AV residue 106 GLU Chi-restraints excluded: chain AW residue 145 ASP Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 14 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BE residue 184 GLU Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 212 ASN Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 338 ILE Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 84 CYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BI residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 1.9990 chunk 180 optimal weight: 0.0470 chunk 269 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 286 optimal weight: 8.9990 chunk 307 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 354 optimal weight: 2.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 131 GLN ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AE 158 GLN AF 71 ASN ** BE 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37817 Z= 0.183 Angle : 0.603 12.755 51257 Z= 0.289 Chirality : 0.036 0.182 5740 Planarity : 0.003 0.057 6586 Dihedral : 7.602 88.768 6390 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.86 % Favored : 98.12 % Rotamer: Outliers : 2.58 % Allowed : 22.76 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.12), residues: 4683 helix: 1.75 (0.09), residues: 3602 sheet: 0.44 (1.09), residues: 26 loop : -0.63 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPBE 158 HIS 0.002 0.001 HISAE 62 PHE 0.012 0.001 PHEAE 59 TYR 0.025 0.001 TYRAY 88 ARG 0.016 0.000 ARGAD 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 569 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9354 (p0) cc_final: 0.9017 (p0) REVERT: AA 105 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7787 (mm-30) REVERT: AA 138 SER cc_start: 0.9067 (m) cc_final: 0.8825 (p) REVERT: AB 28 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8813 (mmmm) REVERT: AB 35 GLU cc_start: 0.8264 (mp0) cc_final: 0.8019 (mp0) REVERT: AB 53 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8612 (tmtm) REVERT: AB 54 GLU cc_start: 0.8344 (tp30) cc_final: 0.8116 (tp30) REVERT: AC 60 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8556 (tm-30) REVERT: AC 61 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8814 (ttmt) REVERT: AC 141 MET cc_start: 0.7109 (pp-130) cc_final: 0.6628 (pp-130) REVERT: AD 2 GLN cc_start: 0.8171 (pm20) cc_final: 0.7860 (pm20) REVERT: AD 17 LYS cc_start: 0.8706 (ptpp) cc_final: 0.8420 (ptpp) REVERT: AD 114 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7699 (pp20) REVERT: AD 131 GLN cc_start: 0.8601 (tt0) cc_final: 0.7792 (tm-30) REVERT: AD 135 GLU cc_start: 0.8562 (mp0) cc_final: 0.7809 (mp0) REVERT: AE 56 LYS cc_start: 0.8591 (tmmt) cc_final: 0.8241 (pptt) REVERT: AE 60 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8783 (tmmm) REVERT: AE 105 GLU cc_start: 0.7797 (tp30) cc_final: 0.7203 (tp30) REVERT: AF 100 ASP cc_start: 0.7663 (t70) cc_final: 0.7291 (t0) REVERT: AK 24 MET cc_start: 0.7844 (mmt) cc_final: 0.7536 (mmt) REVERT: AK 141 MET cc_start: 0.7485 (ttm) cc_final: 0.7227 (ttm) REVERT: AL 1 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7351 (ptt) REVERT: AQ 149 MET cc_start: 0.8737 (mmm) cc_final: 0.8510 (tpp) REVERT: AU 27 LYS cc_start: 0.9096 (ptmm) cc_final: 0.8847 (ptpp) REVERT: AU 115 MET cc_start: 0.8396 (tmm) cc_final: 0.8181 (tmt) REVERT: AU 144 ASP cc_start: 0.7400 (p0) cc_final: 0.6830 (p0) REVERT: AU 145 ASP cc_start: 0.8413 (m-30) cc_final: 0.7816 (m-30) REVERT: AV 1 MET cc_start: 0.7239 (pmm) cc_final: 0.6989 (ppp) REVERT: AV 15 GLN cc_start: 0.8458 (mp10) cc_final: 0.8124 (mp10) REVERT: AV 147 LYS cc_start: 0.9018 (tppp) cc_final: 0.8569 (tppt) REVERT: AW 52 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8692 (ttpp) REVERT: AW 141 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7568 (pp-130) REVERT: BB 3 MET cc_start: 0.8729 (mmt) cc_final: 0.8091 (mmp) REVERT: BB 24 ASN cc_start: 0.8575 (t0) cc_final: 0.8159 (t0) REVERT: BC 44 MET cc_start: 0.7963 (mtt) cc_final: 0.7305 (mtt) REVERT: BE 255 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: BH 174 GLU cc_start: 0.6966 (pt0) cc_final: 0.6387 (pp20) outliers start: 98 outliers final: 54 residues processed: 639 average time/residue: 1.6688 time to fit residues: 1273.5641 Evaluate side-chains 601 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 542 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 49 THR Chi-restraints excluded: chain AA residue 89 LEU Chi-restraints excluded: chain AB residue 53 LYS Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 103 ILE Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 5 THR Chi-restraints excluded: chain AC residue 71 ASN Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AD residue 114 GLU Chi-restraints excluded: chain AD residue 127 VAL Chi-restraints excluded: chain AE residue 85 TYR Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 137 THR Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 49 THR Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 105 LEU Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 1 MET Chi-restraints excluded: chain AL residue 161 SER Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AO residue 100 ASP Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AS residue 133 ILE Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 53 GLN Chi-restraints excluded: chain AU residue 89 LEU Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AU residue 126 VAL Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AW residue 141 MET Chi-restraints excluded: chain AW residue 145 ASP Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 14 THR Chi-restraints excluded: chain BB residue 53 VAL Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BE residue 184 GLU Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 255 GLN Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 338 ILE Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 69 LYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BI residue 117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 410 optimal weight: 0.9980 chunk 432 optimal weight: 0.0770 chunk 394 optimal weight: 0.9990 chunk 420 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 330 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 379 optimal weight: 9.9990 chunk 397 optimal weight: 5.9990 chunk 418 optimal weight: 0.7980 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 80 GLN AE 120 ASN AF 71 ASN BB 24 ASN BC 13 GLN ** BE 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37817 Z= 0.178 Angle : 0.616 11.395 51257 Z= 0.296 Chirality : 0.037 0.213 5740 Planarity : 0.003 0.086 6586 Dihedral : 7.635 88.905 6390 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.96 % Favored : 98.01 % Rotamer: Outliers : 2.14 % Allowed : 23.50 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.12), residues: 4683 helix: 1.85 (0.09), residues: 3564 sheet: 0.50 (1.13), residues: 26 loop : -0.75 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPAE 87 HIS 0.002 0.001 HISAE 62 PHE 0.013 0.001 PHEAE 59 TYR 0.040 0.001 TYRAE 85 ARG 0.020 0.000 ARGAD 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 561 time to evaluate : 4.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9346 (p0) cc_final: 0.9023 (p0) REVERT: AA 105 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7811 (mm-30) REVERT: AA 138 SER cc_start: 0.9061 (m) cc_final: 0.8818 (p) REVERT: AB 28 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8809 (mmmm) REVERT: AB 35 GLU cc_start: 0.8260 (mp0) cc_final: 0.8011 (mp0) REVERT: AB 53 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8569 (tmtm) REVERT: AB 54 GLU cc_start: 0.8393 (tp30) cc_final: 0.8165 (tp30) REVERT: AC 53 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: AC 60 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8551 (tm-30) REVERT: AC 61 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8805 (ttmt) REVERT: AC 141 MET cc_start: 0.6901 (pp-130) cc_final: 0.6389 (pp-130) REVERT: AD 2 GLN cc_start: 0.8105 (pm20) cc_final: 0.7807 (pm20) REVERT: AD 114 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7920 (pp20) REVERT: AD 135 GLU cc_start: 0.8561 (mp0) cc_final: 0.8328 (mp0) REVERT: AE 56 LYS cc_start: 0.8606 (tmmt) cc_final: 0.8267 (pptt) REVERT: AE 60 LYS cc_start: 0.8984 (ttpp) cc_final: 0.8735 (tmmm) REVERT: AE 105 GLU cc_start: 0.7781 (tp30) cc_final: 0.7192 (tp30) REVERT: AF 58 LYS cc_start: 0.9067 (mtpp) cc_final: 0.8767 (mtpt) REVERT: AF 71 ASN cc_start: 0.8399 (t160) cc_final: 0.8190 (t0) REVERT: AF 100 ASP cc_start: 0.7589 (t70) cc_final: 0.7264 (t0) REVERT: AK 141 MET cc_start: 0.7433 (ttm) cc_final: 0.7161 (ttm) REVERT: AN 44 THR cc_start: 0.9070 (m) cc_final: 0.8765 (p) REVERT: AO 24 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7446 (mpt) REVERT: AQ 149 MET cc_start: 0.8749 (mmm) cc_final: 0.8536 (tpp) REVERT: AS 72 MET cc_start: 0.8210 (ttp) cc_final: 0.7954 (ttt) REVERT: AU 144 ASP cc_start: 0.7386 (p0) cc_final: 0.6817 (p0) REVERT: AU 145 ASP cc_start: 0.8414 (m-30) cc_final: 0.7824 (m-30) REVERT: AU 159 LYS cc_start: 0.9479 (mmtm) cc_final: 0.9268 (mmtp) REVERT: AV 1 MET cc_start: 0.7176 (pmm) cc_final: 0.6933 (ppp) REVERT: AV 15 GLN cc_start: 0.8474 (mp10) cc_final: 0.8136 (mp10) REVERT: AW 52 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8699 (ttpp) REVERT: AW 141 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8140 (ptm) REVERT: AZ 149 MET cc_start: 0.9178 (mmm) cc_final: 0.8706 (tpt) REVERT: BB 24 ASN cc_start: 0.8489 (t0) cc_final: 0.8164 (t0) REVERT: BC 44 MET cc_start: 0.7938 (mtt) cc_final: 0.7282 (mtt) outliers start: 81 outliers final: 52 residues processed: 613 average time/residue: 1.6056 time to fit residues: 1176.8413 Evaluate side-chains 596 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 539 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 LEU Chi-restraints excluded: chain AA residue 161 SER Chi-restraints excluded: chain AB residue 53 LYS Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 5 THR Chi-restraints excluded: chain AC residue 24 ASP Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 71 ASN Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 114 GLU Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 25 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 137 THR Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 49 THR Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 105 LEU Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 161 SER Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AO residue 24 MET Chi-restraints excluded: chain AO residue 100 ASP Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AU residue 26 ILE Chi-restraints excluded: chain AU residue 49 THR Chi-restraints excluded: chain AU residue 89 LEU Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AW residue 141 MET Chi-restraints excluded: chain AW residue 145 ASP Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 14 THR Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BE residue 184 GLU Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 304 TYR Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 240 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 69 LYS Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BH residue 176 VAL Chi-restraints excluded: chain BI residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 276 optimal weight: 3.9990 chunk 444 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 308 optimal weight: 8.9990 chunk 466 optimal weight: 6.9990 chunk 429 optimal weight: 0.9980 chunk 371 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 131 GLN ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AQ 15 GLN AR 60 GLN BE 451 ASN BI 96 GLN BI 97 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 37817 Z= 0.181 Angle : 0.624 9.739 51257 Z= 0.301 Chirality : 0.037 0.215 5740 Planarity : 0.003 0.075 6586 Dihedral : 7.635 89.211 6390 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % Rotamer: Outliers : 1.66 % Allowed : 24.02 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.12), residues: 4683 helix: 1.86 (0.09), residues: 3569 sheet: 0.48 (1.11), residues: 26 loop : -0.71 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPBE 158 HIS 0.002 0.001 HISBE 445 PHE 0.012 0.001 PHEBE 424 TYR 0.027 0.001 TYRAD 78 ARG 0.019 0.000 ARGAD 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9366 Ramachandran restraints generated. 4683 Oldfield, 0 Emsley, 4683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 556 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 64 ASP cc_start: 0.9332 (p0) cc_final: 0.9024 (p0) REVERT: AA 105 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7803 (mm-30) REVERT: AA 138 SER cc_start: 0.9059 (m) cc_final: 0.8814 (p) REVERT: AB 28 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8808 (mmmm) REVERT: AB 53 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8540 (tmtm) REVERT: AB 54 GLU cc_start: 0.8382 (tp30) cc_final: 0.8160 (tp30) REVERT: AC 53 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: AC 60 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8539 (tm-30) REVERT: AC 61 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8809 (ttmt) REVERT: AC 141 MET cc_start: 0.6692 (pp-130) cc_final: 0.6151 (pp-130) REVERT: AD 2 GLN cc_start: 0.8028 (pm20) cc_final: 0.7797 (pm20) REVERT: AD 114 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7858 (pp20) REVERT: AD 135 GLU cc_start: 0.8543 (mp0) cc_final: 0.8327 (mp0) REVERT: AE 49 LYS cc_start: 0.8479 (tptp) cc_final: 0.8249 (tptp) REVERT: AE 56 LYS cc_start: 0.8618 (tmmt) cc_final: 0.8256 (pptt) REVERT: AE 60 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8717 (tmmm) REVERT: AE 105 GLU cc_start: 0.7768 (tp30) cc_final: 0.7175 (tp30) REVERT: AF 71 ASN cc_start: 0.8263 (t160) cc_final: 0.8015 (t0) REVERT: AF 72 MET cc_start: 0.8815 (tmm) cc_final: 0.8541 (ttt) REVERT: AF 100 ASP cc_start: 0.7570 (t70) cc_final: 0.7240 (t0) REVERT: AH 161 SER cc_start: 0.7528 (m) cc_final: 0.7288 (p) REVERT: AK 24 MET cc_start: 0.7871 (mmt) cc_final: 0.7523 (mmt) REVERT: AK 141 MET cc_start: 0.7431 (ttm) cc_final: 0.7157 (ttm) REVERT: AN 44 THR cc_start: 0.9037 (m) cc_final: 0.8747 (p) REVERT: AQ 149 MET cc_start: 0.8745 (mmm) cc_final: 0.8524 (tpp) REVERT: AU 144 ASP cc_start: 0.7289 (p0) cc_final: 0.6717 (p0) REVERT: AU 145 ASP cc_start: 0.8383 (m-30) cc_final: 0.7795 (m-30) REVERT: AU 159 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9268 (mmtp) REVERT: AV 1 MET cc_start: 0.7071 (pmm) cc_final: 0.6837 (ppp) REVERT: AV 2 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7226 (tm-30) REVERT: AV 15 GLN cc_start: 0.8467 (mp10) cc_final: 0.8130 (mp10) REVERT: AW 37 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9086 (mm) REVERT: AW 52 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8700 (ttpp) REVERT: AW 141 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7524 (pp-130) REVERT: BB 24 ASN cc_start: 0.8525 (t0) cc_final: 0.8261 (t0) REVERT: BC 44 MET cc_start: 0.7889 (mtt) cc_final: 0.7224 (mtt) REVERT: BH 174 GLU cc_start: 0.6852 (pt0) cc_final: 0.6396 (pp20) outliers start: 63 outliers final: 44 residues processed: 601 average time/residue: 1.6188 time to fit residues: 1160.2846 Evaluate side-chains 587 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 538 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 89 LEU Chi-restraints excluded: chain AB residue 53 LYS Chi-restraints excluded: chain AB residue 74 THR Chi-restraints excluded: chain AB residue 161 SER Chi-restraints excluded: chain AC residue 5 THR Chi-restraints excluded: chain AC residue 24 ASP Chi-restraints excluded: chain AC residue 53 GLN Chi-restraints excluded: chain AC residue 73 TYR Chi-restraints excluded: chain AD residue 114 GLU Chi-restraints excluded: chain AE residue 88 TYR Chi-restraints excluded: chain AF residue 5 ILE Chi-restraints excluded: chain AF residue 20 ASP Chi-restraints excluded: chain AF residue 50 THR Chi-restraints excluded: chain AF residue 139 SER Chi-restraints excluded: chain AH residue 30 VAL Chi-restraints excluded: chain AH residue 49 THR Chi-restraints excluded: chain AH residue 97 VAL Chi-restraints excluded: chain AI residue 65 VAL Chi-restraints excluded: chain AK residue 14 LEU Chi-restraints excluded: chain AK residue 105 LEU Chi-restraints excluded: chain AK residue 169 VAL Chi-restraints excluded: chain AL residue 161 SER Chi-restraints excluded: chain AN residue 97 VAL Chi-restraints excluded: chain AO residue 100 ASP Chi-restraints excluded: chain AP residue 30 VAL Chi-restraints excluded: chain AR residue 5 THR Chi-restraints excluded: chain AR residue 30 VAL Chi-restraints excluded: chain AU residue 26 ILE Chi-restraints excluded: chain AU residue 89 LEU Chi-restraints excluded: chain AU residue 97 VAL Chi-restraints excluded: chain AW residue 37 LEU Chi-restraints excluded: chain AW residue 66 VAL Chi-restraints excluded: chain AW residue 141 MET Chi-restraints excluded: chain AW residue 145 ASP Chi-restraints excluded: chain AZ residue 133 ILE Chi-restraints excluded: chain AZ residue 135 GLU Chi-restraints excluded: chain BB residue 14 THR Chi-restraints excluded: chain BB residue 16 ILE Chi-restraints excluded: chain BB residue 57 THR Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BE residue 212 ASN Chi-restraints excluded: chain BE residue 343 LEU Chi-restraints excluded: chain BE residue 524 VAL Chi-restraints excluded: chain BG residue 225 ILE Chi-restraints excluded: chain BG residue 240 ILE Chi-restraints excluded: chain BG residue 246 VAL Chi-restraints excluded: chain BH residue 15 THR Chi-restraints excluded: chain BH residue 158 VAL Chi-restraints excluded: chain BI residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 294 optimal weight: 10.0000 chunk 395 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 342 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 381 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 131 GLN ** AE 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 80 GLN AE 120 ASN AR 60 GLN BC 13 GLN BI 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049949 restraints weight = 117961.510| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.56 r_work: 0.2877 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37817 Z= 0.181 Angle : 0.622 10.896 51257 Z= 0.300 Chirality : 0.037 0.205 5740 Planarity : 0.003 0.070 6586 Dihedral : 7.639 89.756 6390 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 1.74 % Allowed : 24.26 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.92 (0.13), residues: 4683 helix: 1.88 (0.09), residues: 3556 sheet: -0.27 (0.84), residues: 38 loop : -0.70 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPAE 87 HIS 0.002 0.001 HISBE 445 PHE 0.012 0.001 PHEBE 424 TYR 0.029 0.001 TYRAD 78 ARG 0.019 0.000 ARGAD 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17548.47 seconds wall clock time: 311 minutes 31.98 seconds (18691.98 seconds total)