Starting phenix.real_space_refine on Fri Mar 6 03:45:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n06_9311/03_2026/6n06_9311.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n06_9311/03_2026/6n06_9311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n06_9311/03_2026/6n06_9311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n06_9311/03_2026/6n06_9311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n06_9311/03_2026/6n06_9311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n06_9311/03_2026/6n06_9311.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 132 5.16 5 C 17712 2.51 5 N 5103 2.21 5 O 5250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28197 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1503 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 10, 'TRANS': 190} Chain: "B" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1503 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 10, 'TRANS': 190} Chain: "C" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1503 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 10, 'TRANS': 190} Chain: "GA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "ID" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Time building chain proxies: 6.15, per 1000 atoms: 0.22 Number of scatterers: 28197 At special positions: 0 Unit cell: (100.94, 217.33, 192.61, 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 132 16.00 O 5250 8.00 N 5103 7.00 C 17712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6960 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 42 sheets defined 42.8% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.645A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 101 through 105 removed outlier: 4.106A pdb=" N LEU A 105 " --> pdb=" O TRP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 removed outlier: 3.568A pdb=" N ALA A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 183 removed outlier: 3.838A pdb=" N GLU A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.570A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 removed outlier: 3.659A pdb=" N GLY B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.802A pdb=" N TRP B 102 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG B 103 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 104 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 105 " --> pdb=" O TRP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 143 removed outlier: 3.595A pdb=" N ALA B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.845A pdb=" N LEU C 105 " --> pdb=" O TRP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'GA' and resid 12 through 27 removed outlier: 3.590A pdb=" N VALGA 24 " --> pdb=" O ALAGA 20 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALAGA 27 " --> pdb=" O METGA 23 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 65 removed outlier: 4.074A pdb=" N GLUGA 58 " --> pdb=" O LYSGA 54 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARGGA 62 " --> pdb=" O GLUGA 58 " (cutoff:3.500A) Processing helix chain 'GA' and resid 80 through 87 Processing helix chain 'GB' and resid 12 through 27 removed outlier: 3.686A pdb=" N ALAGB 27 " --> pdb=" O METGB 23 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 65 removed outlier: 3.561A pdb=" N GLUGB 58 " --> pdb=" O LYSGB 54 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARGGB 62 " --> pdb=" O GLUGB 58 " (cutoff:3.500A) Processing helix chain 'GB' and resid 80 through 87 Processing helix chain 'GC' and resid 12 through 27 removed outlier: 3.542A pdb=" N ALAGC 27 " --> pdb=" O METGC 23 " (cutoff:3.500A) Processing helix chain 'GC' and resid 49 through 65 removed outlier: 3.640A pdb=" N GLUGC 58 " --> pdb=" O LYSGC 54 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARGGC 62 " --> pdb=" O GLUGC 58 " (cutoff:3.500A) Processing helix chain 'GC' and resid 80 through 87 Processing helix chain 'GD' and resid 12 through 27 removed outlier: 3.629A pdb=" N VALGD 24 " --> pdb=" O ALAGD 20 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALAGD 27 " --> pdb=" O METGD 23 " (cutoff:3.500A) Processing helix chain 'GD' and resid 49 through 65 removed outlier: 3.810A pdb=" N GLUGD 58 " --> pdb=" O LYSGD 54 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARGGD 62 " --> pdb=" O GLUGD 58 " (cutoff:3.500A) Processing helix chain 'GD' and resid 80 through 87 Processing helix chain 'GE' and resid 12 through 27 removed outlier: 3.680A pdb=" N VALGE 24 " --> pdb=" O ALAGE 20 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALAGE 27 " --> pdb=" O METGE 23 " (cutoff:3.500A) Processing helix chain 'GE' and resid 49 through 65 removed outlier: 3.810A pdb=" N GLUGE 58 " --> pdb=" O LYSGE 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARGGE 62 " --> pdb=" O GLUGE 58 " (cutoff:3.500A) Processing helix chain 'GE' and resid 80 through 87 Processing helix chain 'GF' and resid 12 through 27 removed outlier: 3.534A pdb=" N METGF 16 " --> pdb=" O GLYGF 12 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VALGF 24 " --> pdb=" O ALAGF 20 " (cutoff:3.500A) Processing helix chain 'GF' and resid 49 through 65 removed outlier: 3.707A pdb=" N GLUGF 58 " --> pdb=" O LYSGF 54 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARGGF 62 " --> pdb=" O GLUGF 58 " (cutoff:3.500A) Processing helix chain 'GF' and resid 80 through 87 Processing helix chain 'HA' and resid 12 through 27 removed outlier: 3.526A pdb=" N METHA 16 " --> pdb=" O GLYHA 12 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VALHA 24 " --> pdb=" O ALAHA 20 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALAHA 27 " --> pdb=" O METHA 23 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 65 removed outlier: 3.644A pdb=" N GLUHA 58 " --> pdb=" O LYSHA 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARGHA 62 " --> pdb=" O GLUHA 58 " (cutoff:3.500A) Processing helix chain 'HB' and resid 12 through 27 removed outlier: 3.543A pdb=" N ALAHB 27 " --> pdb=" O METHB 23 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 65 removed outlier: 3.811A pdb=" N GLUHB 58 " --> pdb=" O LYSHB 54 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARGHB 62 " --> pdb=" O GLUHB 58 " (cutoff:3.500A) Processing helix chain 'HB' and resid 80 through 87 Processing helix chain 'HC' and resid 12 through 27 removed outlier: 3.590A pdb=" N VALHC 24 " --> pdb=" O ALAHC 20 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALAHC 27 " --> pdb=" O METHC 23 " (cutoff:3.500A) Processing helix chain 'HC' and resid 49 through 65 removed outlier: 3.878A pdb=" N GLUHC 58 " --> pdb=" O LYSHC 54 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARGHC 62 " --> pdb=" O GLUHC 58 " (cutoff:3.500A) Processing helix chain 'HC' and resid 80 through 87 Processing helix chain 'HD' and resid 12 through 27 removed outlier: 3.600A pdb=" N METHD 16 " --> pdb=" O GLYHD 12 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VALHD 24 " --> pdb=" O ALAHD 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALAHD 27 " --> pdb=" O METHD 23 " (cutoff:3.500A) Processing helix chain 'HD' and resid 49 through 65 removed outlier: 3.701A pdb=" N GLUHD 58 " --> pdb=" O LYSHD 54 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARGHD 62 " --> pdb=" O GLUHD 58 " (cutoff:3.500A) Processing helix chain 'HD' and resid 80 through 87 Processing helix chain 'HE' and resid 12 through 27 removed outlier: 3.542A pdb=" N ALAHE 27 " --> pdb=" O METHE 23 " (cutoff:3.500A) Processing helix chain 'HE' and resid 49 through 65 removed outlier: 3.646A pdb=" N GLUHE 58 " --> pdb=" O LYSHE 54 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARGHE 62 " --> pdb=" O GLUHE 58 " (cutoff:3.500A) Processing helix chain 'HE' and resid 80 through 87 Processing helix chain 'HF' and resid 12 through 27 removed outlier: 3.595A pdb=" N VALHF 24 " --> pdb=" O ALAHF 20 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALAHF 27 " --> pdb=" O METHF 23 " (cutoff:3.500A) Processing helix chain 'HF' and resid 49 through 65 removed outlier: 3.749A pdb=" N GLUHF 58 " --> pdb=" O LYSHF 54 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARGHF 62 " --> pdb=" O GLUHF 58 " (cutoff:3.500A) Processing helix chain 'HF' and resid 80 through 87 Processing helix chain 'IA' and resid 12 through 27 removed outlier: 3.603A pdb=" N VALIA 24 " --> pdb=" O ALAIA 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALAIA 27 " --> pdb=" O METIA 23 " (cutoff:3.500A) Processing helix chain 'IA' and resid 49 through 65 removed outlier: 3.981A pdb=" N GLUIA 58 " --> pdb=" O LYSIA 54 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARGIA 62 " --> pdb=" O GLUIA 58 " (cutoff:3.500A) Processing helix chain 'IA' and resid 80 through 87 Processing helix chain 'IB' and resid 12 through 27 removed outlier: 3.605A pdb=" N VALIB 24 " --> pdb=" O ALAIB 20 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALAIB 27 " --> pdb=" O METIB 23 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 65 removed outlier: 3.566A pdb=" N GLUIB 58 " --> pdb=" O LYSIB 54 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARGIB 62 " --> pdb=" O GLUIB 58 " (cutoff:3.500A) Processing helix chain 'IB' and resid 80 through 87 Processing helix chain 'IC' and resid 12 through 27 removed outlier: 3.647A pdb=" N ALAIC 27 " --> pdb=" O METIC 23 " (cutoff:3.500A) Processing helix chain 'IC' and resid 49 through 65 removed outlier: 3.670A pdb=" N GLUIC 58 " --> pdb=" O LYSIC 54 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARGIC 62 " --> pdb=" O GLUIC 58 " (cutoff:3.500A) Processing helix chain 'IC' and resid 80 through 87 Processing helix chain 'ID' and resid 12 through 27 removed outlier: 3.633A pdb=" N ALAID 27 " --> pdb=" O METID 23 " (cutoff:3.500A) Processing helix chain 'ID' and resid 49 through 65 removed outlier: 3.803A pdb=" N GLUID 58 " --> pdb=" O LYSID 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGID 62 " --> pdb=" O GLUID 58 " (cutoff:3.500A) Processing helix chain 'ID' and resid 80 through 87 Processing helix chain 'IE' and resid 12 through 27 removed outlier: 3.706A pdb=" N VALIE 24 " --> pdb=" O ALAIE 20 " (cutoff:3.500A) Processing helix chain 'IE' and resid 49 through 65 removed outlier: 3.771A pdb=" N GLUIE 58 " --> pdb=" O LYSIE 54 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARGIE 62 " --> pdb=" O GLUIE 58 " (cutoff:3.500A) Processing helix chain 'IE' and resid 80 through 87 Processing helix chain 'IF' and resid 12 through 27 removed outlier: 3.511A pdb=" N VALIF 24 " --> pdb=" O ALAIF 20 " (cutoff:3.500A) Processing helix chain 'IF' and resid 49 through 65 removed outlier: 3.721A pdb=" N GLUIF 58 " --> pdb=" O LYSIF 54 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARGIF 62 " --> pdb=" O GLUIF 58 " (cutoff:3.500A) Processing helix chain 'IF' and resid 80 through 87 Processing helix chain 'JA' and resid 12 through 27 removed outlier: 3.608A pdb=" N VALJA 24 " --> pdb=" O ALAJA 20 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 65 removed outlier: 3.855A pdb=" N GLUJA 58 " --> pdb=" O LYSJA 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARGJA 62 " --> pdb=" O GLUJA 58 " (cutoff:3.500A) Processing helix chain 'JA' and resid 80 through 87 Processing helix chain 'JB' and resid 12 through 27 removed outlier: 3.524A pdb=" N VALJB 24 " --> pdb=" O ALAJB 20 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALAJB 27 " --> pdb=" O METJB 23 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 65 removed outlier: 3.829A pdb=" N GLUJB 58 " --> pdb=" O LYSJB 54 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARGJB 62 " --> pdb=" O GLUJB 58 " (cutoff:3.500A) Processing helix chain 'JB' and resid 80 through 87 Processing helix chain 'JC' and resid 12 through 27 removed outlier: 3.540A pdb=" N VALJC 24 " --> pdb=" O ALAJC 20 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALAJC 27 " --> pdb=" O METJC 23 " (cutoff:3.500A) Processing helix chain 'JC' and resid 49 through 65 removed outlier: 3.974A pdb=" N GLUJC 58 " --> pdb=" O LYSJC 54 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARGJC 62 " --> pdb=" O GLUJC 58 " (cutoff:3.500A) Processing helix chain 'JC' and resid 80 through 87 Processing helix chain 'JD' and resid 12 through 27 removed outlier: 3.772A pdb=" N ALAJD 27 " --> pdb=" O METJD 23 " (cutoff:3.500A) Processing helix chain 'JD' and resid 49 through 65 removed outlier: 3.695A pdb=" N GLUJD 58 " --> pdb=" O LYSJD 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARGJD 62 " --> pdb=" O GLUJD 58 " (cutoff:3.500A) Processing helix chain 'JD' and resid 80 through 87 Processing helix chain 'JE' and resid 12 through 27 removed outlier: 3.632A pdb=" N ALAJE 27 " --> pdb=" O METJE 23 " (cutoff:3.500A) Processing helix chain 'JE' and resid 49 through 65 removed outlier: 3.547A pdb=" N GLUJE 58 " --> pdb=" O LYSJE 54 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARGJE 62 " --> pdb=" O GLUJE 58 " (cutoff:3.500A) Processing helix chain 'JE' and resid 80 through 87 Processing helix chain 'JF' and resid 12 through 27 removed outlier: 3.682A pdb=" N VALJF 24 " --> pdb=" O ALAJF 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALAJF 27 " --> pdb=" O METJF 23 " (cutoff:3.500A) Processing helix chain 'JF' and resid 49 through 65 removed outlier: 3.780A pdb=" N GLUJF 58 " --> pdb=" O LYSJF 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARGJF 62 " --> pdb=" O GLUJF 58 " (cutoff:3.500A) Processing helix chain 'JF' and resid 80 through 87 Processing helix chain 'KA' and resid 12 through 27 removed outlier: 3.511A pdb=" N METKA 16 " --> pdb=" O GLYKA 12 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VALKA 24 " --> pdb=" O ALAKA 20 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 65 removed outlier: 3.907A pdb=" N GLUKA 58 " --> pdb=" O LYSKA 54 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGKA 62 " --> pdb=" O GLUKA 58 " (cutoff:3.500A) Processing helix chain 'KA' and resid 80 through 87 Processing helix chain 'KB' and resid 12 through 27 removed outlier: 3.528A pdb=" N VALKB 24 " --> pdb=" O ALAKB 20 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAKB 27 " --> pdb=" O METKB 23 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 65 removed outlier: 3.864A pdb=" N ARGKB 62 " --> pdb=" O GLUKB 58 " (cutoff:3.500A) Processing helix chain 'KB' and resid 80 through 87 Processing helix chain 'KC' and resid 12 through 27 removed outlier: 3.506A pdb=" N VALKC 24 " --> pdb=" O ALAKC 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAKC 27 " --> pdb=" O METKC 23 " (cutoff:3.500A) Processing helix chain 'KC' and resid 49 through 65 removed outlier: 3.732A pdb=" N GLUKC 58 " --> pdb=" O LYSKC 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARGKC 62 " --> pdb=" O GLUKC 58 " (cutoff:3.500A) Processing helix chain 'KC' and resid 80 through 87 Processing helix chain 'KD' and resid 12 through 27 removed outlier: 3.592A pdb=" N ALAKD 27 " --> pdb=" O METKD 23 " (cutoff:3.500A) Processing helix chain 'KD' and resid 49 through 65 removed outlier: 3.891A pdb=" N GLUKD 58 " --> pdb=" O LYSKD 54 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARGKD 62 " --> pdb=" O GLUKD 58 " (cutoff:3.500A) Processing helix chain 'KD' and resid 80 through 87 Processing helix chain 'KE' and resid 12 through 27 removed outlier: 3.798A pdb=" N VALKE 24 " --> pdb=" O ALAKE 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALAKE 27 " --> pdb=" O METKE 23 " (cutoff:3.500A) Processing helix chain 'KE' and resid 49 through 65 removed outlier: 3.813A pdb=" N GLUKE 58 " --> pdb=" O LYSKE 54 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARGKE 62 " --> pdb=" O GLUKE 58 " (cutoff:3.500A) Processing helix chain 'KE' and resid 80 through 87 Processing helix chain 'KF' and resid 12 through 27 removed outlier: 3.851A pdb=" N VALKF 24 " --> pdb=" O ALAKF 20 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYSKF 25 " --> pdb=" O ASPKF 21 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALAKF 26 " --> pdb=" O ALAKF 22 " (cutoff:3.500A) Processing helix chain 'KF' and resid 49 through 65 removed outlier: 3.846A pdb=" N GLUKF 58 " --> pdb=" O LYSKF 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARGKF 62 " --> pdb=" O GLUKF 58 " (cutoff:3.500A) Processing helix chain 'KF' and resid 80 through 87 Processing helix chain 'LA' and resid 12 through 27 removed outlier: 3.548A pdb=" N VALLA 24 " --> pdb=" O ALALA 20 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 65 removed outlier: 3.771A pdb=" N GLULA 58 " --> pdb=" O LYSLA 54 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARGLA 62 " --> pdb=" O GLULA 58 " (cutoff:3.500A) Processing helix chain 'LA' and resid 80 through 87 Processing helix chain 'LB' and resid 12 through 27 removed outlier: 3.576A pdb=" N ALALB 27 " --> pdb=" O METLB 23 " (cutoff:3.500A) Processing helix chain 'LB' and resid 49 through 65 removed outlier: 3.854A pdb=" N GLULB 58 " --> pdb=" O LYSLB 54 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARGLB 62 " --> pdb=" O GLULB 58 " (cutoff:3.500A) Processing helix chain 'LB' and resid 80 through 87 Processing helix chain 'LC' and resid 12 through 27 removed outlier: 3.579A pdb=" N ALALC 27 " --> pdb=" O METLC 23 " (cutoff:3.500A) Processing helix chain 'LC' and resid 49 through 65 removed outlier: 3.944A pdb=" N GLULC 58 " --> pdb=" O LYSLC 54 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARGLC 62 " --> pdb=" O GLULC 58 " (cutoff:3.500A) Processing helix chain 'LC' and resid 80 through 87 Processing helix chain 'LD' and resid 12 through 27 removed outlier: 3.567A pdb=" N METLD 16 " --> pdb=" O GLYLD 12 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VALLD 24 " --> pdb=" O ALALD 20 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALALD 27 " --> pdb=" O METLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 49 through 65 removed outlier: 3.734A pdb=" N GLULD 58 " --> pdb=" O LYSLD 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARGLD 62 " --> pdb=" O GLULD 58 " (cutoff:3.500A) Processing helix chain 'LD' and resid 80 through 87 Processing helix chain 'LE' and resid 12 through 27 removed outlier: 3.616A pdb=" N ALALE 27 " --> pdb=" O METLE 23 " (cutoff:3.500A) Processing helix chain 'LE' and resid 49 through 65 removed outlier: 3.657A pdb=" N GLULE 58 " --> pdb=" O LYSLE 54 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARGLE 62 " --> pdb=" O GLULE 58 " (cutoff:3.500A) Processing helix chain 'LE' and resid 80 through 87 Processing helix chain 'LF' and resid 12 through 27 removed outlier: 3.609A pdb=" N VALLF 24 " --> pdb=" O ALALF 20 " (cutoff:3.500A) Processing helix chain 'LF' and resid 49 through 65 removed outlier: 3.856A pdb=" N GLULF 58 " --> pdb=" O LYSLF 54 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARGLF 62 " --> pdb=" O GLULF 58 " (cutoff:3.500A) Processing helix chain 'LF' and resid 80 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 6.356A pdb=" N MET A 62 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 51 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 60 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS A 58 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 65 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 90 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 152 removed outlier: 5.641A pdb=" N LEU A 147 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 165 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 149 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 121 " --> pdb=" O CYS A 191 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N CYS A 191 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE A 123 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 189 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU A 125 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 54 removed outlier: 6.391A pdb=" N MET B 62 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 51 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 60 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS B 58 " --> pdb=" O PRO B 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 22 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 93 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 24 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU B 91 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU B 26 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 152 removed outlier: 5.825A pdb=" N LEU B 147 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR B 165 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP B 149 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 121 " --> pdb=" O CYS B 191 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N CYS B 191 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE B 123 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU B 189 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLU B 125 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 54 removed outlier: 6.329A pdb=" N MET C 62 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER C 51 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 60 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS C 58 " --> pdb=" O PRO C 53 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY C 65 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 90 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 152 removed outlier: 5.536A pdb=" N LEU C 147 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 165 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP C 149 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL C 121 " --> pdb=" O CYS C 191 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N CYS C 191 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE C 123 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU C 189 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLU C 125 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'GA' and resid 31 through 36 removed outlier: 5.872A pdb=" N LEUGA 31 " --> pdb=" O ARGGA 47 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARGGA 47 " --> pdb=" O LEUGA 31 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLYGA 33 " --> pdb=" O VALGA 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VALGA 45 " --> pdb=" O GLYGA 33 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HISGA 74 " --> pdb=" O METGA 7 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALAGA 72 " --> pdb=" O GLUGA 9 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARGGA 11 " --> pdb=" O VALGA 70 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VALGA 70 " --> pdb=" O ARGGA 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'GB' and resid 30 through 38 removed outlier: 5.683A pdb=" N LEUGB 31 " --> pdb=" O ARGGB 47 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARGGB 47 " --> pdb=" O LEUGB 31 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLYGB 33 " --> pdb=" O VALGB 45 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VALGB 45 " --> pdb=" O GLYGB 33 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYRGB 41 " --> pdb=" O THRGB 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALAGB 72 " --> pdb=" O GLUGB 9 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARGGB 11 " --> pdb=" O VALGB 70 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VALGB 70 " --> pdb=" O ARGGB 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'GC' and resid 30 through 36 removed outlier: 5.573A pdb=" N LEUGC 31 " --> pdb=" O ARGGC 47 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARGGC 47 " --> pdb=" O LEUGC 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLYGC 33 " --> pdb=" O VALGC 45 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VALGC 45 " --> pdb=" O GLYGC 33 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALAGC 72 " --> pdb=" O GLUGC 9 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARGGC 11 " --> pdb=" O VALGC 70 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VALGC 70 " --> pdb=" O ARGGC 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'GD' and resid 30 through 38 removed outlier: 5.803A pdb=" N LEUGD 31 " --> pdb=" O ARGGD 47 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARGGD 47 " --> pdb=" O LEUGD 31 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLYGD 33 " --> pdb=" O VALGD 45 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VALGD 45 " --> pdb=" O GLYGD 33 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYRGD 41 " --> pdb=" O THRGD 37 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALAGD 72 " --> pdb=" O GLUGD 9 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARGGD 11 " --> pdb=" O VALGD 70 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VALGD 70 " --> pdb=" O ARGGD 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'GE' and resid 31 through 38 removed outlier: 5.968A pdb=" N LEUGE 31 " --> pdb=" O ARGGE 47 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARGGE 47 " --> pdb=" O LEUGE 31 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLYGE 33 " --> pdb=" O VALGE 45 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VALGE 45 " --> pdb=" O GLYGE 33 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYRGE 41 " --> pdb=" O THRGE 37 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALAGE 72 " --> pdb=" O GLUGE 9 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARGGE 11 " --> pdb=" O VALGE 70 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VALGE 70 " --> pdb=" O ARGGE 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'GF' and resid 30 through 38 removed outlier: 5.740A pdb=" N LEUGF 31 " --> pdb=" O ARGGF 47 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARGGF 47 " --> pdb=" O LEUGF 31 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLYGF 33 " --> pdb=" O VALGF 45 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VALGF 45 " --> pdb=" O GLYGF 33 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYRGF 41 " --> pdb=" O THRGF 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HISGF 74 " --> pdb=" O METGF 7 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAGF 72 " --> pdb=" O GLUGF 9 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARGGF 11 " --> pdb=" O VALGF 70 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VALGF 70 " --> pdb=" O ARGGF 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'HA' and resid 30 through 36 removed outlier: 5.641A pdb=" N LEUHA 31 " --> pdb=" O ARGHA 47 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARGHA 47 " --> pdb=" O LEUHA 31 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLYHA 33 " --> pdb=" O VALHA 45 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VALHA 45 " --> pdb=" O GLYHA 33 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HISHA 74 " --> pdb=" O METHA 7 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALAHA 72 " --> pdb=" O GLUHA 9 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARGHA 11 " --> pdb=" O VALHA 70 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VALHA 70 " --> pdb=" O ARGHA 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'HB' and resid 30 through 38 removed outlier: 5.731A pdb=" N LEUHB 31 " --> pdb=" O ARGHB 47 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARGHB 47 " --> pdb=" O LEUHB 31 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLYHB 33 " --> pdb=" O VALHB 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VALHB 45 " --> pdb=" O GLYHB 33 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THRHB 37 " --> pdb=" O TYRHB 41 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYRHB 41 " --> pdb=" O THRHB 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALAHB 72 " --> pdb=" O GLUHB 9 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARGHB 11 " --> pdb=" O VALHB 70 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VALHB 70 " --> pdb=" O ARGHB 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'HC' and resid 30 through 38 removed outlier: 5.620A pdb=" N LEUHC 31 " --> pdb=" O ARGHC 47 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARGHC 47 " --> pdb=" O LEUHC 31 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLYHC 33 " --> pdb=" O VALHC 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VALHC 45 " --> pdb=" O GLYHC 33 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYRHC 41 " --> pdb=" O THRHC 37 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HISHC 74 " --> pdb=" O METHC 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALAHC 72 " --> pdb=" O GLUHC 9 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARGHC 11 " --> pdb=" O VALHC 70 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VALHC 70 " --> pdb=" O ARGHC 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'HD' and resid 30 through 36 removed outlier: 5.617A pdb=" N LEUHD 31 " --> pdb=" O ARGHD 47 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARGHD 47 " --> pdb=" O LEUHD 31 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLYHD 33 " --> pdb=" O VALHD 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HISHD 74 " --> pdb=" O METHD 7 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALAHD 72 " --> pdb=" O GLUHD 9 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARGHD 11 " --> pdb=" O VALHD 70 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VALHD 70 " --> pdb=" O ARGHD 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'HE' and resid 30 through 36 removed outlier: 5.444A pdb=" N LEUHE 31 " --> pdb=" O ARGHE 47 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARGHE 47 " --> pdb=" O LEUHE 31 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLYHE 33 " --> pdb=" O VALHE 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VALHE 45 " --> pdb=" O GLYHE 33 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALAHE 72 " --> pdb=" O GLUHE 9 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARGHE 11 " --> pdb=" O VALHE 70 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VALHE 70 " --> pdb=" O ARGHE 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'HF' and resid 30 through 38 removed outlier: 5.868A pdb=" N LEUHF 31 " --> pdb=" O ARGHF 47 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARGHF 47 " --> pdb=" O LEUHF 31 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLYHF 33 " --> pdb=" O VALHF 45 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VALHF 45 " --> pdb=" O GLYHF 33 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYRHF 41 " --> pdb=" O THRHF 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HISHF 74 " --> pdb=" O METHF 7 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALAHF 72 " --> pdb=" O GLUHF 9 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARGHF 11 " --> pdb=" O VALHF 70 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VALHF 70 " --> pdb=" O ARGHF 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'IA' and resid 30 through 38 removed outlier: 5.702A pdb=" N LEUIA 31 " --> pdb=" O ARGIA 47 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARGIA 47 " --> pdb=" O LEUIA 31 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLYIA 33 " --> pdb=" O VALIA 45 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VALIA 45 " --> pdb=" O GLYIA 33 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYRIA 41 " --> pdb=" O THRIA 37 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEUIA 5 " --> pdb=" O VALIA 75 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VALIA 75 " --> pdb=" O LEUIA 5 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N METIA 7 " --> pdb=" O VALIA 73 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VALIA 73 " --> pdb=" O METIA 7 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLUIA 9 " --> pdb=" O VALIA 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'IB' and resid 30 through 38 removed outlier: 5.615A pdb=" N LEUIB 31 " --> pdb=" O ARGIB 47 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARGIB 47 " --> pdb=" O LEUIB 31 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLYIB 33 " --> pdb=" O VALIB 45 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYRIB 41 " --> pdb=" O THRIB 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HISIB 74 " --> pdb=" O METIB 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALAIB 72 " --> pdb=" O GLUIB 9 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARGIB 11 " --> pdb=" O VALIB 70 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VALIB 70 " --> pdb=" O ARGIB 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'IC' and resid 31 through 36 removed outlier: 5.868A pdb=" N LEUIC 31 " --> pdb=" O ARGIC 47 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARGIC 47 " --> pdb=" O LEUIC 31 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLYIC 33 " --> pdb=" O VALIC 45 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VALIC 45 " --> pdb=" O GLYIC 33 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALAIC 72 " --> pdb=" O GLUIC 9 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARGIC 11 " --> pdb=" O VALIC 70 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VALIC 70 " --> pdb=" O ARGIC 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'ID' and resid 30 through 38 removed outlier: 5.852A pdb=" N LEUID 31 " --> pdb=" O ARGID 47 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARGID 47 " --> pdb=" O LEUID 31 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLYID 33 " --> pdb=" O VALID 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VALID 45 " --> pdb=" O GLYID 33 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYRID 41 " --> pdb=" O THRID 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HISID 74 " --> pdb=" O METID 7 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALAID 72 " --> pdb=" O GLUID 9 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGID 11 " --> pdb=" O VALID 70 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VALID 70 " --> pdb=" O ARGID 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'IE' and resid 31 through 38 removed outlier: 6.082A pdb=" N LEUIE 31 " --> pdb=" O ARGIE 47 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARGIE 47 " --> pdb=" O LEUIE 31 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLYIE 33 " --> pdb=" O VALIE 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VALIE 45 " --> pdb=" O GLYIE 33 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYRIE 41 " --> pdb=" O THRIE 37 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HISIE 74 " --> pdb=" O METIE 7 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALAIE 72 " --> pdb=" O GLUIE 9 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARGIE 11 " --> pdb=" O VALIE 70 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VALIE 70 " --> pdb=" O ARGIE 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'IF' and resid 31 through 38 removed outlier: 5.672A pdb=" N LEUIF 31 " --> pdb=" O ARGIF 47 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARGIF 47 " --> pdb=" O LEUIF 31 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLYIF 33 " --> pdb=" O VALIF 45 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VALIF 45 " --> pdb=" O GLYIF 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THRIF 37 " --> pdb=" O TYRIF 41 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYRIF 41 " --> pdb=" O THRIF 37 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HISIF 74 " --> pdb=" O METIF 7 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALAIF 72 " --> pdb=" O GLUIF 9 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARGIF 11 " --> pdb=" O VALIF 70 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VALIF 70 " --> pdb=" O ARGIF 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'JA' and resid 31 through 38 removed outlier: 5.785A pdb=" N LEUJA 31 " --> pdb=" O ARGJA 47 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARGJA 47 " --> pdb=" O LEUJA 31 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLYJA 33 " --> pdb=" O VALJA 45 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VALJA 45 " --> pdb=" O GLYJA 33 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYRJA 41 " --> pdb=" O THRJA 37 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEUJA 5 " --> pdb=" O VALJA 75 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VALJA 75 " --> pdb=" O LEUJA 5 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N METJA 7 " --> pdb=" O VALJA 73 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VALJA 73 " --> pdb=" O METJA 7 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLUJA 9 " --> pdb=" O VALJA 71 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLUJA 69 " --> pdb=" O ARGJA 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'JB' and resid 30 through 38 removed outlier: 5.598A pdb=" N LEUJB 31 " --> pdb=" O ARGJB 47 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ARGJB 47 " --> pdb=" O LEUJB 31 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLYJB 33 " --> pdb=" O VALJB 45 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THRJB 37 " --> pdb=" O TYRJB 41 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N TYRJB 41 " --> pdb=" O THRJB 37 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HISJB 74 " --> pdb=" O METJB 7 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALAJB 72 " --> pdb=" O GLUJB 9 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARGJB 11 " --> pdb=" O VALJB 70 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VALJB 70 " --> pdb=" O ARGJB 11 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'JC' and resid 30 through 38 removed outlier: 5.668A pdb=" N LEUJC 31 " --> pdb=" O ARGJC 47 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ARGJC 47 " --> pdb=" O LEUJC 31 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLYJC 33 " --> pdb=" O VALJC 45 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VALJC 45 " --> pdb=" O GLYJC 33 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYRJC 41 " --> pdb=" O THRJC 37 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HISJC 74 " --> pdb=" O METJC 7 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALAJC 72 " --> pdb=" O GLUJC 9 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARGJC 11 " --> pdb=" O VALJC 70 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VALJC 70 " --> pdb=" O ARGJC 11 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'JD' and resid 30 through 36 removed outlier: 5.688A pdb=" N LEUJD 31 " --> pdb=" O ARGJD 47 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARGJD 47 " --> pdb=" O LEUJD 31 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLYJD 33 " --> pdb=" O VALJD 45 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VALJD 45 " --> pdb=" O GLYJD 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HISJD 74 " --> pdb=" O METJD 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALAJD 72 " --> pdb=" O GLUJD 9 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARGJD 11 " --> pdb=" O VALJD 70 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VALJD 70 " --> pdb=" O ARGJD 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'JE' and resid 30 through 36 removed outlier: 5.482A pdb=" N LEUJE 31 " --> pdb=" O ARGJE 47 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARGJE 47 " --> pdb=" O LEUJE 31 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLYJE 33 " --> pdb=" O VALJE 45 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALJE 45 " --> pdb=" O GLYJE 33 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALAJE 72 " --> pdb=" O GLUJE 9 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARGJE 11 " --> pdb=" O VALJE 70 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VALJE 70 " --> pdb=" O ARGJE 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'JF' and resid 30 through 36 removed outlier: 5.936A pdb=" N LEUJF 31 " --> pdb=" O ARGJF 47 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARGJF 47 " --> pdb=" O LEUJF 31 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLYJF 33 " --> pdb=" O VALJF 45 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VALJF 45 " --> pdb=" O GLYJF 33 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HISJF 74 " --> pdb=" O METJF 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALAJF 72 " --> pdb=" O GLUJF 9 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARGJF 11 " --> pdb=" O VALJF 70 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VALJF 70 " --> pdb=" O ARGJF 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'KA' and resid 30 through 36 removed outlier: 5.642A pdb=" N LEUKA 31 " --> pdb=" O ARGKA 47 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARGKA 47 " --> pdb=" O LEUKA 31 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYKA 33 " --> pdb=" O VALKA 45 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VALKA 45 " --> pdb=" O GLYKA 33 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HISKA 74 " --> pdb=" O METKA 7 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALAKA 72 " --> pdb=" O GLUKA 9 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARGKA 11 " --> pdb=" O VALKA 70 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VALKA 70 " --> pdb=" O ARGKA 11 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'KB' and resid 30 through 38 removed outlier: 5.483A pdb=" N LEUKB 31 " --> pdb=" O ARGKB 47 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARGKB 47 " --> pdb=" O LEUKB 31 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLYKB 33 " --> pdb=" O VALKB 45 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VALKB 45 " --> pdb=" O GLYKB 33 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYRKB 41 " --> pdb=" O THRKB 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HISKB 74 " --> pdb=" O METKB 7 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAKB 72 " --> pdb=" O GLUKB 9 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARGKB 11 " --> pdb=" O VALKB 70 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VALKB 70 " --> pdb=" O ARGKB 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'KC' and resid 31 through 36 removed outlier: 3.864A pdb=" N GLYKC 33 " --> pdb=" O VALKC 45 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALKC 45 " --> pdb=" O GLYKC 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HISKC 74 " --> pdb=" O METKC 7 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALAKC 72 " --> pdb=" O GLUKC 9 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARGKC 11 " --> pdb=" O VALKC 70 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VALKC 70 " --> pdb=" O ARGKC 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'KD' and resid 30 through 38 removed outlier: 5.724A pdb=" N LEUKD 31 " --> pdb=" O ARGKD 47 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARGKD 47 " --> pdb=" O LEUKD 31 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLYKD 33 " --> pdb=" O VALKD 45 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VALKD 45 " --> pdb=" O GLYKD 33 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYRKD 41 " --> pdb=" O THRKD 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALAKD 72 " --> pdb=" O GLUKD 9 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARGKD 11 " --> pdb=" O VALKD 70 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VALKD 70 " --> pdb=" O ARGKD 11 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'KE' and resid 31 through 38 removed outlier: 6.000A pdb=" N LEUKE 31 " --> pdb=" O ARGKE 47 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARGKE 47 " --> pdb=" O LEUKE 31 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLYKE 33 " --> pdb=" O VALKE 45 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VALKE 45 " --> pdb=" O GLYKE 33 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYRKE 41 " --> pdb=" O THRKE 37 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HISKE 74 " --> pdb=" O METKE 7 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAKE 72 " --> pdb=" O GLUKE 9 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARGKE 11 " --> pdb=" O VALKE 70 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VALKE 70 " --> pdb=" O ARGKE 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'KF' and resid 30 through 36 removed outlier: 5.692A pdb=" N LEUKF 31 " --> pdb=" O ARGKF 47 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARGKF 47 " --> pdb=" O LEUKF 31 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLYKF 33 " --> pdb=" O VALKF 45 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HISKF 74 " --> pdb=" O METKF 7 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALAKF 72 " --> pdb=" O GLUKF 9 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARGKF 11 " --> pdb=" O VALKF 70 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VALKF 70 " --> pdb=" O ARGKF 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LA' and resid 31 through 38 removed outlier: 5.800A pdb=" N LEULA 31 " --> pdb=" O ARGLA 47 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARGLA 47 " --> pdb=" O LEULA 31 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLYLA 33 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYRLA 41 " --> pdb=" O THRLA 37 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HISLA 74 " --> pdb=" O METLA 7 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALALA 72 " --> pdb=" O GLULA 9 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARGLA 11 " --> pdb=" O VALLA 70 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VALLA 70 " --> pdb=" O ARGLA 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'LB' and resid 30 through 36 removed outlier: 5.651A pdb=" N LEULB 31 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARGLB 47 " --> pdb=" O LEULB 31 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLYLB 33 " --> pdb=" O VALLB 45 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VALLB 45 " --> pdb=" O GLYLB 33 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HISLB 74 " --> pdb=" O METLB 7 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALALB 72 " --> pdb=" O GLULB 9 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARGLB 11 " --> pdb=" O VALLB 70 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VALLB 70 " --> pdb=" O ARGLB 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'LC' and resid 30 through 36 removed outlier: 5.765A pdb=" N LEULC 31 " --> pdb=" O ARGLC 47 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ARGLC 47 " --> pdb=" O LEULC 31 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLYLC 33 " --> pdb=" O VALLC 45 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VALLC 45 " --> pdb=" O GLYLC 33 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HISLC 74 " --> pdb=" O METLC 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALALC 72 " --> pdb=" O GLULC 9 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARGLC 11 " --> pdb=" O VALLC 70 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VALLC 70 " --> pdb=" O ARGLC 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'LD' and resid 30 through 38 removed outlier: 5.678A pdb=" N LEULD 31 " --> pdb=" O ARGLD 47 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARGLD 47 " --> pdb=" O LEULD 31 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLYLD 33 " --> pdb=" O VALLD 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VALLD 45 " --> pdb=" O GLYLD 33 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYRLD 41 " --> pdb=" O THRLD 37 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HISLD 74 " --> pdb=" O METLD 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALALD 72 " --> pdb=" O GLULD 9 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARGLD 11 " --> pdb=" O VALLD 70 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VALLD 70 " --> pdb=" O ARGLD 11 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'LE' and resid 30 through 36 removed outlier: 5.612A pdb=" N LEULE 31 " --> pdb=" O ARGLE 47 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARGLE 47 " --> pdb=" O LEULE 31 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLYLE 33 " --> pdb=" O VALLE 45 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VALLE 45 " --> pdb=" O GLYLE 33 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALALE 72 " --> pdb=" O GLULE 9 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARGLE 11 " --> pdb=" O VALLE 70 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VALLE 70 " --> pdb=" O ARGLE 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'LF' and resid 30 through 38 removed outlier: 5.853A pdb=" N LEULF 31 " --> pdb=" O ARGLF 47 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARGLF 47 " --> pdb=" O LEULF 31 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLYLF 33 " --> pdb=" O VALLF 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VALLF 45 " --> pdb=" O GLYLF 33 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYRLF 41 " --> pdb=" O THRLF 37 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HISLF 74 " --> pdb=" O METLF 7 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALALF 72 " --> pdb=" O GLULF 9 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARGLF 11 " --> pdb=" O VALLF 70 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VALLF 70 " --> pdb=" O ARGLF 11 " (cutoff:3.500A) 1650 hydrogen bonds defined for protein. 4803 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: 4.87 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9825 1.34 - 1.46: 4270 1.46 - 1.58: 14204 1.58 - 1.69: 0 1.69 - 1.81: 255 Bond restraints: 28554 Sorted by residual: bond pdb=" CB VAL A 36 " pdb=" CG1 VAL A 36 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 bond pdb=" CB VAL B 36 " pdb=" CG1 VAL B 36 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.05e+00 bond pdb=" CG1 ILE A 34 " pdb=" CD1 ILE A 34 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.01e+00 bond pdb=" CB ARGHE 47 " pdb=" CG ARGHE 47 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB ARGLA 47 " pdb=" CG ARGLA 47 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.60e+00 ... (remaining 28549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 37154 1.67 - 3.34: 1442 3.34 - 5.01: 141 5.01 - 6.68: 24 6.68 - 8.35: 2 Bond angle restraints: 38763 Sorted by residual: angle pdb=" N ILE C 30 " pdb=" CA ILE C 30 " pdb=" C ILE C 30 " ideal model delta sigma weight residual 112.96 108.60 4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" C LEU C 152 " pdb=" N ALA C 153 " pdb=" CA ALA C 153 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C LEU A 152 " pdb=" N ALA A 153 " pdb=" CA ALA A 153 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" CA TRP B 114 " pdb=" C TRP B 114 " pdb=" N GLU B 115 " ideal model delta sigma weight residual 115.75 120.02 -4.27 1.34e+00 5.57e-01 1.02e+01 angle pdb=" C ALA B 37 " pdb=" N ASP B 38 " pdb=" CA ASP B 38 " ideal model delta sigma weight residual 121.14 115.90 5.24 1.75e+00 3.27e-01 8.96e+00 ... (remaining 38758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.49: 15724 9.49 - 18.97: 1173 18.97 - 28.46: 195 28.46 - 37.95: 123 37.95 - 47.44: 41 Dihedral angle restraints: 17256 sinusoidal: 6345 harmonic: 10911 Sorted by residual: dihedral pdb=" CA ASPHD 49 " pdb=" C ASPHD 49 " pdb=" N VALHD 50 " pdb=" CA VALHD 50 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASPJD 49 " pdb=" C ASPJD 49 " pdb=" N VALJD 50 " pdb=" CA VALJD 50 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ASPHE 49 " pdb=" C ASPHE 49 " pdb=" N VALHE 50 " pdb=" CA VALHE 50 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 17253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3307 0.050 - 0.101: 988 0.101 - 0.151: 332 0.151 - 0.201: 32 0.201 - 0.252: 9 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CB ILE C 123 " pdb=" CA ILE C 123 " pdb=" CG1 ILE C 123 " pdb=" CG2 ILE C 123 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE A 123 " pdb=" CA ILE A 123 " pdb=" CG1 ILE A 123 " pdb=" CG2 ILE A 123 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE C 154 " pdb=" CA ILE C 154 " pdb=" CG1 ILE C 154 " pdb=" CG2 ILE C 154 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 4665 not shown) Planarity restraints: 5097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILELB 76 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PROLB 77 " -0.095 5.00e-02 4.00e+02 pdb=" CA PROLB 77 " 0.028 5.00e-02 4.00e+02 pdb=" CD PROLB 77 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEHF 76 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PROHF 77 " -0.089 5.00e-02 4.00e+02 pdb=" CA PROHF 77 " 0.026 5.00e-02 4.00e+02 pdb=" CD PROHF 77 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEJB 76 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PROJB 77 " 0.088 5.00e-02 4.00e+02 pdb=" CA PROJB 77 " -0.026 5.00e-02 4.00e+02 pdb=" CD PROJB 77 " -0.028 5.00e-02 4.00e+02 ... (remaining 5094 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4990 2.77 - 3.30: 24533 3.30 - 3.84: 46582 3.84 - 4.37: 53726 4.37 - 4.90: 96658 Nonbonded interactions: 226489 Sorted by model distance: nonbonded pdb=" OD1 ASP A 149 " pdb=" OG1 THR A 163 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP C 149 " pdb=" OG1 THR C 163 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP B 149 " pdb=" OG1 THR B 163 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OE2 GLU A 99 " model vdw 2.325 3.040 nonbonded pdb=" OG SER B 120 " pdb=" O ILE B 192 " model vdw 2.333 3.040 ... (remaining 226484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'GA' selection = chain 'GB' selection = chain 'GC' selection = chain 'GD' selection = chain 'GE' selection = chain 'GF' selection = chain 'HA' selection = chain 'HB' selection = chain 'HC' selection = chain 'HD' selection = chain 'HE' selection = chain 'HF' selection = chain 'IA' selection = chain 'IB' selection = chain 'IC' selection = chain 'ID' selection = chain 'IE' selection = chain 'IF' selection = chain 'JA' selection = chain 'JB' selection = chain 'JC' selection = chain 'JD' selection = chain 'JE' selection = chain 'JF' selection = chain 'KA' selection = chain 'KB' selection = chain 'KC' selection = chain 'KD' selection = chain 'KE' selection = chain 'KF' selection = chain 'LA' selection = chain 'LB' selection = chain 'LC' selection = chain 'LD' selection = chain 'LE' selection = chain 'LF' } 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: 8.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.860 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.005 0.055 28554 Z= 0.220 Angle : 0.736 8.346 38763 Z= 0.417 Chirality : 0.053 0.252 4668 Planarity : 0.006 0.055 5097 Dihedral : 8.243 47.437 10296 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.12), residues: 3837 helix: -3.55 (0.08), residues: 1596 sheet: -0.74 (0.15), residues: 1146 loop : -2.92 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 185 TYR 0.022 0.004 TYRHE 34 PHE 0.022 0.004 PHE C 205 TRP 0.011 0.002 TRP C 114 HIS 0.005 0.001 HISLA 74 Details of bonding type rmsd covalent geometry : bond 0.00537 (28554) covalent geometry : angle 0.73612 (38763) hydrogen bonds : bond 0.15383 ( 1650) hydrogen bonds : angle 6.24465 ( 4803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 899 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: GA 10 VAL cc_start: 0.9339 (t) cc_final: 0.8824 (p) REVERT: GC 10 VAL cc_start: 0.9298 (t) cc_final: 0.9055 (m) REVERT: GD 16 MET cc_start: 0.9147 (tmm) cc_final: 0.8635 (tmm) REVERT: GD 43 THR cc_start: 0.9140 (m) cc_final: 0.8874 (p) REVERT: HD 78 ARG cc_start: 0.7062 (mmm160) cc_final: 0.6802 (mtm-85) REVERT: HE 10 VAL cc_start: 0.9176 (t) cc_final: 0.8522 (p) REVERT: HF 16 MET cc_start: 0.8829 (tmm) cc_final: 0.8347 (tmm) REVERT: IB 16 MET cc_start: 0.8818 (tmm) cc_final: 0.8568 (tmm) REVERT: IB 58 GLU cc_start: 0.7590 (pt0) cc_final: 0.7369 (pt0) REVERT: IC 28 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8297 (mmtm) REVERT: IC 61 GLN cc_start: 0.8878 (tt0) cc_final: 0.8619 (tt0) REVERT: JA 28 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8263 (tttm) REVERT: JA 78 ARG cc_start: 0.7831 (tpt170) cc_final: 0.7569 (tpp-160) REVERT: JC 30 GLU cc_start: 0.8550 (tt0) cc_final: 0.8332 (tt0) REVERT: JE 84 ASP cc_start: 0.8414 (m-30) cc_final: 0.8178 (m-30) REVERT: JF 43 THR cc_start: 0.9139 (m) cc_final: 0.8933 (m) REVERT: KA 62 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7959 (mtm110) REVERT: KC 28 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8314 (mmtm) REVERT: KC 54 LYS cc_start: 0.8393 (tttm) cc_final: 0.8145 (tptt) REVERT: KC 61 GLN cc_start: 0.8675 (tt0) cc_final: 0.8397 (tt0) REVERT: KD 16 MET cc_start: 0.9222 (tmm) cc_final: 0.8974 (tmm) REVERT: KD 78 ARG cc_start: 0.7129 (mmm160) cc_final: 0.6764 (mtm-85) REVERT: LA 16 MET cc_start: 0.8843 (tmm) cc_final: 0.8579 (tmm) REVERT: LA 28 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8155 (tttp) REVERT: LC 41 TYR cc_start: 0.8868 (m-10) cc_final: 0.8467 (m-80) REVERT: LC 54 LYS cc_start: 0.8081 (tttm) cc_final: 0.7877 (mmtt) REVERT: LC 58 GLU cc_start: 0.8062 (pt0) cc_final: 0.7860 (mt-10) REVERT: LD 16 MET cc_start: 0.9129 (tmm) cc_final: 0.8808 (tmm) REVERT: LD 78 ARG cc_start: 0.6947 (mmm160) cc_final: 0.6343 (mtm-85) REVERT: LF 16 MET cc_start: 0.8983 (tmm) cc_final: 0.8512 (tmm) outliers start: 1 outliers final: 0 residues processed: 899 average time/residue: 0.2549 time to fit residues: 323.1782 Evaluate side-chains 639 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN C 100 GLN GD 82 ASN GE 82 ASN HB 82 ASN HC 82 ASN HF 82 ASN IA 82 ASN IB 82 ASN IC 82 ASN IE 82 ASN JC 82 ASN JE 61 GLN JE 82 ASN JF 82 ASN KA 82 ASN KB 82 ASN KE 82 ASN KF 82 ASN LB 82 ASN LC 82 ASN LE 82 ASN LF 82 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.092382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.083037 restraints weight = 42513.031| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.75 r_work: 0.2774 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28554 Z= 0.179 Angle : 0.592 8.147 38763 Z= 0.319 Chirality : 0.046 0.193 4668 Planarity : 0.005 0.056 5097 Dihedral : 4.609 22.756 4215 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.21 % Allowed : 9.64 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 3837 helix: -1.16 (0.12), residues: 1599 sheet: 0.24 (0.16), residues: 1002 loop : -2.88 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGGA 47 TYR 0.011 0.002 TYRKF 41 PHE 0.012 0.001 PHE A 161 TRP 0.009 0.001 TRP B 102 HIS 0.003 0.001 HISJF 80 Details of bonding type rmsd covalent geometry : bond 0.00426 (28554) covalent geometry : angle 0.59158 (38763) hydrogen bonds : bond 0.04172 ( 1650) hydrogen bonds : angle 4.45068 ( 4803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 695 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: C 58 LYS cc_start: 0.8625 (mttm) cc_final: 0.8421 (mtmt) REVERT: GA 92 THR cc_start: 0.9290 (m) cc_final: 0.9025 (p) REVERT: GC 11 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8100 (ttt90) REVERT: GD 43 THR cc_start: 0.9319 (m) cc_final: 0.9066 (t) REVERT: GE 7 MET cc_start: 0.9128 (mtm) cc_final: 0.8873 (mtm) REVERT: GE 54 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8432 (ttpp) REVERT: GF 21 ASP cc_start: 0.8847 (t70) cc_final: 0.8626 (t0) REVERT: HC 3 ASP cc_start: 0.8506 (m-30) cc_final: 0.8148 (m-30) REVERT: HC 54 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8143 (mtmt) REVERT: HD 78 ARG cc_start: 0.7819 (mmm160) cc_final: 0.6674 (mtm-85) REVERT: HE 11 ARG cc_start: 0.8732 (ttt-90) cc_final: 0.8156 (ttt90) REVERT: IC 28 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8268 (mmtm) REVERT: ID 9 GLU cc_start: 0.8800 (tt0) cc_final: 0.8586 (tt0) REVERT: JA 28 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8360 (tttp) REVERT: JB 11 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8625 (ttt-90) REVERT: JB 36 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8709 (mttt) REVERT: JC 30 GLU cc_start: 0.8953 (tt0) cc_final: 0.8734 (tt0) REVERT: JC 54 LYS cc_start: 0.8669 (tptt) cc_final: 0.7498 (mtpt) REVERT: JD 54 LYS cc_start: 0.8835 (tptp) cc_final: 0.8608 (tptp) REVERT: JF 43 THR cc_start: 0.9324 (m) cc_final: 0.9083 (m) REVERT: KC 28 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8356 (mmtm) REVERT: KD 78 ARG cc_start: 0.8099 (mmm160) cc_final: 0.6676 (mtm-85) REVERT: KE 28 LYS cc_start: 0.9175 (tttm) cc_final: 0.8872 (tttp) REVERT: KE 62 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7828 (ttp-110) REVERT: LA 7 MET cc_start: 0.9117 (mtt) cc_final: 0.8845 (mtt) REVERT: LA 16 MET cc_start: 0.9107 (tmm) cc_final: 0.8832 (tmm) REVERT: LA 28 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8291 (tttp) REVERT: LC 11 ARG cc_start: 0.8554 (ttt90) cc_final: 0.8211 (ttt90) REVERT: LC 54 LYS cc_start: 0.8326 (tttm) cc_final: 0.8033 (mmtt) REVERT: LC 58 GLU cc_start: 0.8643 (pt0) cc_final: 0.8040 (mt-10) REVERT: LD 16 MET cc_start: 0.9408 (tmm) cc_final: 0.9173 (tmm) REVERT: LD 34 TYR cc_start: 0.9170 (p90) cc_final: 0.8878 (p90) outliers start: 33 outliers final: 18 residues processed: 710 average time/residue: 0.2399 time to fit residues: 244.0550 Evaluate side-chains 662 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 643 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain GE residue 54 LYS Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain IA residue 58 GLU Chi-restraints excluded: chain IC residue 10 VAL Chi-restraints excluded: chain ID residue 3 ASP Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain KA residue 58 GLU Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KD residue 58 GLU Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 34 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 367 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 323 optimal weight: 0.9980 chunk 291 optimal weight: 0.0170 chunk 110 optimal weight: 0.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: GA 82 ASN HD 82 ASN JB 82 ASN LB 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.091037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.081501 restraints weight = 42664.761| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.82 r_work: 0.2700 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28554 Z= 0.178 Angle : 0.576 8.361 38763 Z= 0.309 Chirality : 0.045 0.177 4668 Planarity : 0.004 0.041 5097 Dihedral : 4.375 21.336 4215 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.24 % Allowed : 10.89 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3837 helix: -0.18 (0.13), residues: 1563 sheet: -0.06 (0.15), residues: 1215 loop : -2.15 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 181 TYR 0.012 0.001 TYRGB 41 PHE 0.010 0.001 PHE B 161 TRP 0.008 0.001 TRP B 102 HIS 0.003 0.001 HISGB 74 Details of bonding type rmsd covalent geometry : bond 0.00428 (28554) covalent geometry : angle 0.57604 (38763) hydrogen bonds : bond 0.03995 ( 1650) hydrogen bonds : angle 4.16519 ( 4803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 659 time to evaluate : 1.058 Fit side-chains REVERT: C 58 LYS cc_start: 0.8558 (mttm) cc_final: 0.8311 (mtmt) REVERT: GA 10 VAL cc_start: 0.9361 (t) cc_final: 0.9113 (m) REVERT: GA 92 THR cc_start: 0.9296 (m) cc_final: 0.9040 (p) REVERT: GC 11 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8350 (ttt180) REVERT: GD 43 THR cc_start: 0.9363 (m) cc_final: 0.9143 (t) REVERT: GE 8 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8917 (tp) REVERT: HA 11 ARG cc_start: 0.9004 (ttt-90) cc_final: 0.8704 (ttt-90) REVERT: HA 54 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8120 (mtmt) REVERT: HC 3 ASP cc_start: 0.8578 (m-30) cc_final: 0.8231 (m-30) REVERT: HC 54 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8159 (mtmt) REVERT: HD 78 ARG cc_start: 0.8067 (mmm160) cc_final: 0.6797 (mtm-85) REVERT: HE 10 VAL cc_start: 0.9307 (t) cc_final: 0.9102 (m) REVERT: HE 41 TYR cc_start: 0.9503 (m-80) cc_final: 0.9266 (m-80) REVERT: HE 69 GLU cc_start: 0.8143 (tt0) cc_final: 0.7885 (pt0) REVERT: IA 10 VAL cc_start: 0.9024 (t) cc_final: 0.8783 (m) REVERT: IA 11 ARG cc_start: 0.8842 (ttm-80) cc_final: 0.8323 (ttt-90) REVERT: IA 58 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: IC 28 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8267 (mmtm) REVERT: ID 9 GLU cc_start: 0.8956 (tt0) cc_final: 0.8679 (tt0) REVERT: JA 28 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8293 (tttp) REVERT: JA 78 ARG cc_start: 0.8613 (tpt90) cc_final: 0.8373 (tpp-160) REVERT: JB 36 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8602 (mttt) REVERT: JC 30 GLU cc_start: 0.8994 (tt0) cc_final: 0.8765 (tt0) REVERT: JC 54 LYS cc_start: 0.8510 (tptt) cc_final: 0.7525 (mtpt) REVERT: JD 37 THR cc_start: 0.9423 (p) cc_final: 0.9211 (m) REVERT: JD 54 LYS cc_start: 0.8719 (tptp) cc_final: 0.8516 (tptp) REVERT: JE 58 GLU cc_start: 0.8346 (pt0) cc_final: 0.7783 (mm-30) REVERT: JF 54 LYS cc_start: 0.8717 (mttm) cc_final: 0.7811 (mtpp) REVERT: JF 58 GLU cc_start: 0.8030 (pt0) cc_final: 0.7605 (pt0) REVERT: KC 28 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8606 (tppt) REVERT: KC 58 GLU cc_start: 0.8412 (pt0) cc_final: 0.8211 (pt0) REVERT: KD 78 ARG cc_start: 0.8115 (mmm160) cc_final: 0.6415 (mtm-85) REVERT: KE 62 ARG cc_start: 0.8212 (ttp-110) cc_final: 0.7893 (ttp-110) REVERT: LA 16 MET cc_start: 0.9084 (tmm) cc_final: 0.8825 (tmm) REVERT: LA 28 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8256 (tttp) REVERT: LB 11 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8272 (ttm-80) REVERT: LB 54 LYS cc_start: 0.8700 (tptt) cc_final: 0.8498 (mttm) REVERT: LC 41 TYR cc_start: 0.9287 (m-80) cc_final: 0.8911 (m-80) REVERT: LC 54 LYS cc_start: 0.8411 (tttm) cc_final: 0.8027 (mmtt) REVERT: LC 58 GLU cc_start: 0.8706 (pt0) cc_final: 0.8015 (mt-10) REVERT: LD 34 TYR cc_start: 0.9157 (p90) cc_final: 0.8909 (p90) REVERT: LD 78 ARG cc_start: 0.8040 (mmm160) cc_final: 0.6430 (mtm-85) REVERT: LE 34 TYR cc_start: 0.9134 (p90) cc_final: 0.8906 (p90) outliers start: 61 outliers final: 39 residues processed: 697 average time/residue: 0.2421 time to fit residues: 242.7500 Evaluate side-chains 663 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 621 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HB residue 42 VAL Chi-restraints excluded: chain HB residue 67 VAL Chi-restraints excluded: chain HC residue 67 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain IA residue 54 LYS Chi-restraints excluded: chain IA residue 58 GLU Chi-restraints excluded: chain IA residue 67 VAL Chi-restraints excluded: chain IC residue 10 VAL Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JB residue 42 VAL Chi-restraints excluded: chain JD residue 42 VAL Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JF residue 42 VAL Chi-restraints excluded: chain KA residue 58 GLU Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 42 VAL Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LC residue 67 VAL Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 288 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 350 optimal weight: 0.1980 chunk 64 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 332 optimal weight: 0.3980 chunk 117 optimal weight: 0.7980 chunk 318 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: HD 82 ASN KB 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.091249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.082097 restraints weight = 42429.265| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.72 r_work: 0.2708 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28554 Z= 0.158 Angle : 0.556 6.587 38763 Z= 0.297 Chirality : 0.045 0.187 4668 Planarity : 0.004 0.039 5097 Dihedral : 4.226 20.507 4215 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.79 % Allowed : 11.22 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3837 helix: 0.31 (0.14), residues: 1563 sheet: 0.96 (0.17), residues: 927 loop : -2.20 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGLF 47 TYR 0.011 0.001 TYRJC 41 PHE 0.010 0.001 PHE B 161 TRP 0.006 0.001 TRP B 102 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00380 (28554) covalent geometry : angle 0.55574 (38763) hydrogen bonds : bond 0.03765 ( 1650) hydrogen bonds : angle 4.01086 ( 4803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 645 time to evaluate : 0.803 Fit side-chains REVERT: B 202 ARG cc_start: 0.7819 (ptm160) cc_final: 0.7471 (ptm160) REVERT: GA 10 VAL cc_start: 0.9360 (t) cc_final: 0.9126 (m) REVERT: GA 92 THR cc_start: 0.9289 (m) cc_final: 0.9077 (p) REVERT: GB 25 LYS cc_start: 0.8377 (mttt) cc_final: 0.8133 (mttt) REVERT: GC 11 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8316 (ttt180) REVERT: GE 8 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8911 (tp) REVERT: GE 25 LYS cc_start: 0.8657 (mttt) cc_final: 0.8409 (mttt) REVERT: HA 54 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8126 (mtmt) REVERT: HB 36 LYS cc_start: 0.8982 (mtmt) cc_final: 0.8678 (mttt) REVERT: HB 65 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8499 (mt-10) REVERT: HC 3 ASP cc_start: 0.8575 (m-30) cc_final: 0.8230 (m-30) REVERT: HC 54 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8141 (mtmt) REVERT: HD 78 ARG cc_start: 0.8155 (mmm160) cc_final: 0.6814 (mtm-85) REVERT: HE 10 VAL cc_start: 0.9334 (t) cc_final: 0.9115 (m) REVERT: HE 11 ARG cc_start: 0.8744 (ttt-90) cc_final: 0.8292 (ttt90) REVERT: HE 65 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8137 (mm-30) REVERT: HF 32 ILE cc_start: 0.9304 (pp) cc_final: 0.9090 (pp) REVERT: HF 58 GLU cc_start: 0.8479 (tp30) cc_final: 0.8223 (tp30) REVERT: IA 58 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: IC 28 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8292 (mmtm) REVERT: IF 5 LEU cc_start: 0.9129 (tp) cc_final: 0.8923 (tp) REVERT: JA 28 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8373 (tttp) REVERT: JA 78 ARG cc_start: 0.8705 (tpt90) cc_final: 0.8432 (tpp-160) REVERT: JC 30 GLU cc_start: 0.9019 (tt0) cc_final: 0.8779 (tt0) REVERT: JD 37 THR cc_start: 0.9402 (p) cc_final: 0.9179 (m) REVERT: JE 58 GLU cc_start: 0.8236 (pt0) cc_final: 0.7747 (mm-30) REVERT: KC 28 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8600 (tppt) REVERT: KC 66 ARG cc_start: 0.8570 (mtp85) cc_final: 0.8167 (mtp-110) REVERT: KD 78 ARG cc_start: 0.8320 (mmm160) cc_final: 0.6382 (mtm-85) REVERT: KE 8 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9148 (tt) REVERT: KE 36 LYS cc_start: 0.9257 (mtmt) cc_final: 0.9038 (mtmt) REVERT: LA 16 MET cc_start: 0.9067 (tmm) cc_final: 0.8794 (tmm) REVERT: LA 28 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8263 (tttp) REVERT: LB 16 MET cc_start: 0.9053 (tmm) cc_final: 0.8815 (tmm) REVERT: LB 43 THR cc_start: 0.9359 (m) cc_final: 0.9083 (m) REVERT: LB 54 LYS cc_start: 0.8653 (tptt) cc_final: 0.8448 (mttm) REVERT: LC 41 TYR cc_start: 0.9265 (m-80) cc_final: 0.9036 (m-80) REVERT: LC 54 LYS cc_start: 0.8507 (tttm) cc_final: 0.8075 (mmtt) REVERT: LC 58 GLU cc_start: 0.8679 (pt0) cc_final: 0.8065 (mt-10) REVERT: LD 34 TYR cc_start: 0.9011 (p90) cc_final: 0.8656 (p90) REVERT: LD 78 ARG cc_start: 0.8112 (mmm160) cc_final: 0.6422 (mtm-85) REVERT: LE 34 TYR cc_start: 0.9151 (p90) cc_final: 0.8919 (p90) REVERT: LE 66 ARG cc_start: 0.8628 (mtp85) cc_final: 0.8311 (ptm160) outliers start: 76 outliers final: 51 residues processed: 695 average time/residue: 0.2429 time to fit residues: 243.7757 Evaluate side-chains 678 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 623 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 67 VAL Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HB residue 42 VAL Chi-restraints excluded: chain HB residue 67 VAL Chi-restraints excluded: chain HC residue 67 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain IA residue 54 LYS Chi-restraints excluded: chain IA residue 58 GLU Chi-restraints excluded: chain IA residue 67 VAL Chi-restraints excluded: chain IC residue 10 VAL Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 3 ASP Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 42 VAL Chi-restraints excluded: chain JB residue 81 VAL Chi-restraints excluded: chain JC residue 67 VAL Chi-restraints excluded: chain JD residue 42 VAL Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JF residue 42 VAL Chi-restraints excluded: chain KA residue 58 GLU Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KA residue 87 LEU Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 42 VAL Chi-restraints excluded: chain KE residue 8 ILE Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LC residue 67 VAL Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LF residue 32 ILE Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 320 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 382 optimal weight: 0.0050 chunk 116 optimal weight: 0.3980 chunk 313 optimal weight: 1.9990 chunk 362 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 317 optimal weight: 0.6980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: KF 82 ASN LB 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.091652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.082199 restraints weight = 42314.659| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.81 r_work: 0.2725 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28554 Z= 0.144 Angle : 0.538 6.382 38763 Z= 0.288 Chirality : 0.044 0.167 4668 Planarity : 0.004 0.040 5097 Dihedral : 4.109 20.120 4215 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.82 % Allowed : 11.84 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3837 helix: 0.60 (0.14), residues: 1563 sheet: 1.16 (0.17), residues: 927 loop : -2.00 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 181 TYR 0.011 0.001 TYRGB 41 PHE 0.009 0.001 PHE B 161 TRP 0.005 0.001 TRP B 102 HIS 0.002 0.001 HISHE 74 Details of bonding type rmsd covalent geometry : bond 0.00343 (28554) covalent geometry : angle 0.53787 (38763) hydrogen bonds : bond 0.03648 ( 1650) hydrogen bonds : angle 3.88606 ( 4803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 639 time to evaluate : 1.002 Fit side-chains REVERT: B 90 ASP cc_start: 0.8396 (t0) cc_final: 0.7937 (m-30) REVERT: GA 10 VAL cc_start: 0.9371 (t) cc_final: 0.9149 (m) REVERT: GA 92 THR cc_start: 0.9280 (m) cc_final: 0.9069 (p) REVERT: GB 7 MET cc_start: 0.8945 (mtm) cc_final: 0.8636 (mtm) REVERT: GB 25 LYS cc_start: 0.8426 (mttt) cc_final: 0.8179 (mttt) REVERT: GD 78 ARG cc_start: 0.8282 (mmm160) cc_final: 0.6087 (mtt90) REVERT: GE 8 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8911 (tp) REVERT: HA 54 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8159 (mtmt) REVERT: HB 36 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8539 (mttt) REVERT: HB 65 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8516 (mt-10) REVERT: HC 3 ASP cc_start: 0.8522 (m-30) cc_final: 0.8194 (m-30) REVERT: HC 54 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8048 (mtmt) REVERT: HD 78 ARG cc_start: 0.8325 (mmm160) cc_final: 0.6934 (mtm-85) REVERT: HE 10 VAL cc_start: 0.9371 (t) cc_final: 0.9158 (m) REVERT: HE 11 ARG cc_start: 0.8744 (ttt-90) cc_final: 0.8305 (ttt90) REVERT: IA 11 ARG cc_start: 0.8882 (ttm-80) cc_final: 0.8370 (ttt-90) REVERT: IA 58 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8264 (tm-30) REVERT: IC 28 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8285 (mmtm) REVERT: IE 8 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.9020 (tt) REVERT: JA 28 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8414 (tttp) REVERT: JB 36 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8608 (mttt) REVERT: JC 30 GLU cc_start: 0.9044 (tt0) cc_final: 0.8816 (tt0) REVERT: JD 54 LYS cc_start: 0.8656 (tptp) cc_final: 0.8409 (tptt) REVERT: JE 58 GLU cc_start: 0.8232 (pt0) cc_final: 0.7791 (mm-30) REVERT: KA 58 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: KB 36 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8879 (mtpp) REVERT: KC 28 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8355 (mmtm) REVERT: KC 58 GLU cc_start: 0.8285 (pt0) cc_final: 0.7998 (pt0) REVERT: KC 66 ARG cc_start: 0.8633 (mtp85) cc_final: 0.8229 (mtp-110) REVERT: KD 78 ARG cc_start: 0.8498 (mmm160) cc_final: 0.6459 (mtm-85) REVERT: KE 36 LYS cc_start: 0.9195 (mtmt) cc_final: 0.8901 (mtmt) REVERT: LA 16 MET cc_start: 0.9086 (tmm) cc_final: 0.8816 (tmm) REVERT: LA 28 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8287 (tttp) REVERT: LB 43 THR cc_start: 0.9367 (m) cc_final: 0.9071 (m) REVERT: LB 58 GLU cc_start: 0.8587 (pt0) cc_final: 0.8153 (tp30) REVERT: LC 3 ASP cc_start: 0.8484 (m-30) cc_final: 0.8053 (m-30) REVERT: LC 54 LYS cc_start: 0.8539 (tttm) cc_final: 0.8153 (mmtt) REVERT: LC 58 GLU cc_start: 0.8695 (pt0) cc_final: 0.8106 (mt-10) REVERT: LD 78 ARG cc_start: 0.8209 (mmm160) cc_final: 0.6570 (mtm-85) REVERT: LE 9 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8773 (tt0) REVERT: LE 34 TYR cc_start: 0.9147 (p90) cc_final: 0.8837 (p90) REVERT: LE 66 ARG cc_start: 0.8641 (mtp85) cc_final: 0.8349 (ptm160) outliers start: 77 outliers final: 47 residues processed: 692 average time/residue: 0.2397 time to fit residues: 239.6150 Evaluate side-chains 667 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 614 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 67 VAL Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GF residue 67 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HB residue 42 VAL Chi-restraints excluded: chain HB residue 67 VAL Chi-restraints excluded: chain HC residue 67 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain IA residue 54 LYS Chi-restraints excluded: chain IA residue 58 GLU Chi-restraints excluded: chain IA residue 67 VAL Chi-restraints excluded: chain IC residue 10 VAL Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 3 ASP Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain IE residue 8 ILE Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 42 VAL Chi-restraints excluded: chain JB residue 81 VAL Chi-restraints excluded: chain JC residue 67 VAL Chi-restraints excluded: chain JD residue 42 VAL Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JF residue 42 VAL Chi-restraints excluded: chain KA residue 58 GLU Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KA residue 87 LEU Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KC residue 42 VAL Chi-restraints excluded: chain KD residue 42 VAL Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LC residue 67 VAL Chi-restraints excluded: chain LE residue 9 GLU Chi-restraints excluded: chain LF residue 32 ILE Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 31 optimal weight: 1.9990 chunk 242 optimal weight: 0.0470 chunk 24 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 351 optimal weight: 0.0870 chunk 187 optimal weight: 0.8980 chunk 267 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 217 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: HD 82 ASN JB 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.092399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.083253 restraints weight = 42311.968| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.72 r_work: 0.2732 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28554 Z= 0.129 Angle : 0.532 6.157 38763 Z= 0.284 Chirality : 0.044 0.163 4668 Planarity : 0.003 0.040 5097 Dihedral : 4.024 19.905 4215 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.71 % Allowed : 12.47 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3837 helix: 0.81 (0.14), residues: 1563 sheet: 1.29 (0.17), residues: 927 loop : -1.84 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGIC 62 TYR 0.009 0.001 TYRGB 41 PHE 0.009 0.001 PHE B 161 TRP 0.004 0.001 TRP B 102 HIS 0.002 0.001 HISJE 74 Details of bonding type rmsd covalent geometry : bond 0.00306 (28554) covalent geometry : angle 0.53175 (38763) hydrogen bonds : bond 0.03523 ( 1650) hydrogen bonds : angle 3.82059 ( 4803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 634 time to evaluate : 1.074 Fit side-chains REVERT: A 60 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8516 (mp) REVERT: B 32 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7426 (ptp-110) REVERT: B 90 ASP cc_start: 0.8370 (t0) cc_final: 0.7913 (m-30) REVERT: C 58 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8429 (mtmt) REVERT: GA 10 VAL cc_start: 0.9359 (t) cc_final: 0.9123 (m) REVERT: GA 92 THR cc_start: 0.9255 (m) cc_final: 0.9050 (p) REVERT: GB 25 LYS cc_start: 0.8378 (mttt) cc_final: 0.8125 (mttt) REVERT: GC 62 ARG cc_start: 0.8319 (ttp-110) cc_final: 0.8018 (mtm110) REVERT: GD 78 ARG cc_start: 0.8315 (mmm160) cc_final: 0.6196 (mtt90) REVERT: GE 8 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8897 (tp) REVERT: GE 41 TYR cc_start: 0.9159 (m-80) cc_final: 0.8597 (m-80) REVERT: HA 54 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8131 (mtmt) REVERT: HB 36 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8506 (mttt) REVERT: HC 3 ASP cc_start: 0.8495 (m-30) cc_final: 0.8117 (m-30) REVERT: HD 78 ARG cc_start: 0.8318 (mmm160) cc_final: 0.6885 (mtm-85) REVERT: HE 11 ARG cc_start: 0.8857 (ttt-90) cc_final: 0.8361 (ttt90) REVERT: HF 54 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8286 (mttt) REVERT: IA 58 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: IC 28 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8288 (mmtm) REVERT: JA 28 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8412 (tttp) REVERT: JB 36 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8588 (mttt) REVERT: JB 82 ASN cc_start: 0.9072 (t0) cc_final: 0.8604 (t0) REVERT: JC 30 GLU cc_start: 0.9005 (tt0) cc_final: 0.8760 (tt0) REVERT: JD 54 LYS cc_start: 0.8592 (tptp) cc_final: 0.8327 (tptt) REVERT: JE 58 GLU cc_start: 0.8265 (pt0) cc_final: 0.7802 (mm-30) REVERT: KA 58 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: KB 36 LYS cc_start: 0.9152 (mtpp) cc_final: 0.8825 (mtpp) REVERT: KC 28 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8602 (tppt) REVERT: KC 58 GLU cc_start: 0.8319 (pt0) cc_final: 0.8042 (pt0) REVERT: KC 66 ARG cc_start: 0.8660 (mtp85) cc_final: 0.8238 (mtp-110) REVERT: KD 78 ARG cc_start: 0.8654 (mmm160) cc_final: 0.6720 (mtm180) REVERT: LA 16 MET cc_start: 0.9070 (tmm) cc_final: 0.8785 (tmm) REVERT: LA 28 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8252 (tttp) REVERT: LB 11 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8181 (ttm-80) REVERT: LB 43 THR cc_start: 0.9347 (m) cc_final: 0.9061 (m) REVERT: LB 58 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8157 (tp30) REVERT: LC 3 ASP cc_start: 0.8426 (m-30) cc_final: 0.7995 (m-30) REVERT: LC 41 TYR cc_start: 0.9293 (m-80) cc_final: 0.9068 (m-80) REVERT: LC 54 LYS cc_start: 0.8462 (tttm) cc_final: 0.8075 (mmtt) REVERT: LC 58 GLU cc_start: 0.8786 (pt0) cc_final: 0.8188 (mt-10) REVERT: LD 78 ARG cc_start: 0.8196 (mmm160) cc_final: 0.6466 (mtm-85) REVERT: LE 9 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8763 (tt0) REVERT: LE 34 TYR cc_start: 0.9106 (p90) cc_final: 0.8820 (p90) REVERT: LE 66 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8367 (ptm160) outliers start: 74 outliers final: 48 residues processed: 681 average time/residue: 0.2372 time to fit residues: 234.2976 Evaluate side-chains 672 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 615 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 67 VAL Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain GF residue 67 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 42 VAL Chi-restraints excluded: chain HB residue 67 VAL Chi-restraints excluded: chain HC residue 67 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HF residue 54 LYS Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 54 LYS Chi-restraints excluded: chain IA residue 58 GLU Chi-restraints excluded: chain IA residue 67 VAL Chi-restraints excluded: chain IC residue 10 VAL Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 3 ASP Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 42 VAL Chi-restraints excluded: chain JC residue 67 VAL Chi-restraints excluded: chain JD residue 42 VAL Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JF residue 42 VAL Chi-restraints excluded: chain KA residue 58 GLU Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KA residue 87 LEU Chi-restraints excluded: chain KD residue 42 VAL Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LB residue 58 GLU Chi-restraints excluded: chain LC residue 67 VAL Chi-restraints excluded: chain LE residue 9 GLU Chi-restraints excluded: chain LF residue 32 ILE Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 292 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 268 optimal weight: 0.1980 chunk 322 optimal weight: 0.6980 chunk 382 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 260 optimal weight: 0.6980 chunk 348 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: GB 82 ASN KB 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.090660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.081459 restraints weight = 42373.858| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.73 r_work: 0.2698 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28554 Z= 0.167 Angle : 0.555 6.636 38763 Z= 0.296 Chirality : 0.045 0.164 4668 Planarity : 0.004 0.035 5097 Dihedral : 4.042 20.410 4215 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.08 % Allowed : 12.43 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3837 helix: 0.80 (0.14), residues: 1563 sheet: 1.34 (0.17), residues: 927 loop : -1.80 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGJB 11 TYR 0.014 0.001 TYRGB 41 PHE 0.010 0.001 PHE B 161 TRP 0.006 0.001 TRP B 102 HIS 0.002 0.001 HISGB 74 Details of bonding type rmsd covalent geometry : bond 0.00402 (28554) covalent geometry : angle 0.55475 (38763) hydrogen bonds : bond 0.03716 ( 1650) hydrogen bonds : angle 3.86777 ( 4803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 633 time to evaluate : 0.840 Fit side-chains REVERT: A 177 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8974 (t) REVERT: B 16 GLU cc_start: 0.7856 (tp30) cc_final: 0.7650 (tp30) REVERT: B 32 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7176 (ptp-110) REVERT: B 90 ASP cc_start: 0.8400 (t0) cc_final: 0.7966 (m-30) REVERT: C 58 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8467 (mtmt) REVERT: GA 10 VAL cc_start: 0.9371 (t) cc_final: 0.9169 (m) REVERT: GA 92 THR cc_start: 0.9257 (m) cc_final: 0.9036 (p) REVERT: GB 25 LYS cc_start: 0.8353 (mttt) cc_final: 0.8108 (mttt) REVERT: GC 62 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.8014 (mtm110) REVERT: GD 78 ARG cc_start: 0.8393 (mmm160) cc_final: 0.6151 (mtt90) REVERT: GE 8 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8887 (tp) REVERT: GE 41 TYR cc_start: 0.9246 (m-80) cc_final: 0.8551 (m-80) REVERT: HA 11 ARG cc_start: 0.8922 (ttt-90) cc_final: 0.8462 (ttt-90) REVERT: HA 54 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: HB 36 LYS cc_start: 0.8989 (mtmt) cc_final: 0.8545 (mttt) REVERT: HC 3 ASP cc_start: 0.8509 (m-30) cc_final: 0.8160 (m-30) REVERT: HC 35 GLU cc_start: 0.8781 (tp30) cc_final: 0.8556 (tp30) REVERT: HD 78 ARG cc_start: 0.8427 (mmm160) cc_final: 0.6943 (mtm-85) REVERT: HE 41 TYR cc_start: 0.9559 (m-80) cc_final: 0.9255 (m-80) REVERT: HF 54 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8286 (mttt) REVERT: IA 11 ARG cc_start: 0.8885 (ttm-80) cc_final: 0.8497 (ttt-90) REVERT: IA 58 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: IC 28 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8308 (mmtm) REVERT: IF 5 LEU cc_start: 0.9056 (tp) cc_final: 0.8848 (tp) REVERT: JA 28 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8442 (tttp) REVERT: JB 36 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8618 (mttt) REVERT: JC 58 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7591 (mp0) REVERT: JD 54 LYS cc_start: 0.8605 (tptp) cc_final: 0.8378 (tptt) REVERT: JE 58 GLU cc_start: 0.8263 (pt0) cc_final: 0.7815 (mm-30) REVERT: KA 58 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: KC 28 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8318 (mmtm) REVERT: KC 58 GLU cc_start: 0.8303 (pt0) cc_final: 0.7965 (pt0) REVERT: KC 66 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8252 (mtp-110) REVERT: KD 78 ARG cc_start: 0.8651 (mmm160) cc_final: 0.6641 (mtm180) REVERT: LA 16 MET cc_start: 0.9020 (tmm) cc_final: 0.8797 (tmm) REVERT: LA 28 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8286 (tttp) REVERT: LB 58 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: LC 3 ASP cc_start: 0.8501 (m-30) cc_final: 0.8069 (m-30) REVERT: LC 41 TYR cc_start: 0.9301 (m-80) cc_final: 0.9043 (m-80) REVERT: LC 54 LYS cc_start: 0.8464 (tttm) cc_final: 0.8043 (mmtt) REVERT: LC 58 GLU cc_start: 0.8748 (pt0) cc_final: 0.8165 (mt-10) REVERT: LD 78 ARG cc_start: 0.8314 (mmm160) cc_final: 0.6573 (mtm-85) REVERT: LE 9 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8768 (tt0) REVERT: LE 34 TYR cc_start: 0.9162 (p90) cc_final: 0.8864 (p90) REVERT: LE 66 ARG cc_start: 0.8660 (mtp85) cc_final: 0.8374 (ptm160) outliers start: 84 outliers final: 62 residues processed: 692 average time/residue: 0.2365 time to fit residues: 236.7656 Evaluate side-chains 681 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 610 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 67 VAL Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain GF residue 67 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 42 VAL Chi-restraints excluded: chain HB residue 67 VAL Chi-restraints excluded: chain HC residue 67 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HF residue 54 LYS Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 54 LYS Chi-restraints excluded: chain IA residue 58 GLU Chi-restraints excluded: chain IA residue 67 VAL Chi-restraints excluded: chain IC residue 10 VAL Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 3 ASP Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 67 VAL Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 42 VAL Chi-restraints excluded: chain JB residue 81 VAL Chi-restraints excluded: chain JC residue 67 VAL Chi-restraints excluded: chain JD residue 42 VAL Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JF residue 42 VAL Chi-restraints excluded: chain KA residue 58 GLU Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KA residue 87 LEU Chi-restraints excluded: chain KB residue 10 VAL Chi-restraints excluded: chain KD residue 42 VAL Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 58 GLU Chi-restraints excluded: chain LC residue 67 VAL Chi-restraints excluded: chain LE residue 9 GLU Chi-restraints excluded: chain LF residue 32 ILE Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 315 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 229 optimal weight: 0.0020 chunk 366 optimal weight: 2.9990 chunk 282 optimal weight: 0.0980 chunk 67 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 206 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.091433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.082001 restraints weight = 42499.124| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.80 r_work: 0.2719 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28554 Z= 0.142 Angle : 0.542 6.279 38763 Z= 0.289 Chirality : 0.044 0.162 4668 Planarity : 0.004 0.049 5097 Dihedral : 3.997 20.040 4215 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.08 % Allowed : 13.09 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3837 helix: 0.88 (0.14), residues: 1563 sheet: 1.38 (0.17), residues: 927 loop : -1.73 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGIC 62 TYR 0.014 0.001 TYRJC 41 PHE 0.009 0.001 PHE A 161 TRP 0.004 0.001 TRP B 102 HIS 0.002 0.001 HISLE 74 Details of bonding type rmsd covalent geometry : bond 0.00339 (28554) covalent geometry : angle 0.54217 (38763) hydrogen bonds : bond 0.03576 ( 1650) hydrogen bonds : angle 3.83106 ( 4803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 617 time to evaluate : 0.995 Fit side-chains REVERT: B 32 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7273 (ptp-110) REVERT: C 58 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8493 (mtmt) REVERT: C 62 MET cc_start: 0.9008 (mtt) cc_final: 0.8799 (mtt) REVERT: GA 10 VAL cc_start: 0.9333 (t) cc_final: 0.9008 (m) REVERT: GA 92 THR cc_start: 0.9245 (m) cc_final: 0.9044 (p) REVERT: GB 25 LYS cc_start: 0.8377 (mttt) cc_final: 0.8120 (mttt) REVERT: GC 62 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.8010 (mtm110) REVERT: GD 78 ARG cc_start: 0.8463 (mmm160) cc_final: 0.6177 (mtt90) REVERT: GE 8 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8882 (tp) REVERT: GE 41 TYR cc_start: 0.9248 (m-80) cc_final: 0.8607 (m-80) REVERT: HA 11 ARG cc_start: 0.8893 (ttt-90) cc_final: 0.8514 (ttt-90) REVERT: HA 54 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8154 (mtmt) REVERT: HB 36 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8503 (mttt) REVERT: HC 3 ASP cc_start: 0.8499 (m-30) cc_final: 0.8147 (m-30) REVERT: HD 78 ARG cc_start: 0.8400 (mmm160) cc_final: 0.6910 (mtm-85) REVERT: HE 11 ARG cc_start: 0.8847 (ttt-90) cc_final: 0.8259 (ttt90) REVERT: HE 23 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8537 (mtp) REVERT: HF 54 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8254 (mttt) REVERT: IC 28 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8312 (mmtm) REVERT: IF 5 LEU cc_start: 0.9032 (tp) cc_final: 0.8811 (tp) REVERT: JA 28 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8428 (tttp) REVERT: JB 36 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8818 (mttt) REVERT: JB 54 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8363 (mtpp) REVERT: JD 54 LYS cc_start: 0.8614 (tptp) cc_final: 0.8372 (tptt) REVERT: JE 58 GLU cc_start: 0.8280 (pt0) cc_final: 0.7845 (mm-30) REVERT: KA 58 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: KC 28 LYS cc_start: 0.8864 (ttpt) cc_final: 0.8322 (mmtm) REVERT: KC 66 ARG cc_start: 0.8661 (mtp85) cc_final: 0.8239 (mtp-110) REVERT: KD 78 ARG cc_start: 0.8683 (mmm160) cc_final: 0.6577 (mtm180) REVERT: LA 28 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8254 (tttp) REVERT: LB 43 THR cc_start: 0.9342 (m) cc_final: 0.9026 (m) REVERT: LB 58 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8252 (tp30) REVERT: LC 3 ASP cc_start: 0.8464 (m-30) cc_final: 0.8026 (m-30) REVERT: LC 54 LYS cc_start: 0.8450 (tttm) cc_final: 0.8052 (mmtt) REVERT: LC 58 GLU cc_start: 0.8793 (pt0) cc_final: 0.8197 (mt-10) REVERT: LD 78 ARG cc_start: 0.8325 (mmm160) cc_final: 0.6485 (mtm180) REVERT: LE 9 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8819 (tt0) REVERT: LE 66 ARG cc_start: 0.8665 (mtp85) cc_final: 0.8388 (ptm160) REVERT: LE 78 ARG cc_start: 0.8695 (tpp80) cc_final: 0.7469 (ptt180) outliers start: 84 outliers final: 60 residues processed: 675 average time/residue: 0.2337 time to fit residues: 230.4482 Evaluate side-chains 672 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 604 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 67 VAL Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain GF residue 67 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 42 VAL Chi-restraints excluded: chain HB residue 67 VAL Chi-restraints excluded: chain HC residue 67 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 23 MET Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HF residue 54 LYS Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 54 LYS Chi-restraints excluded: chain IA residue 67 VAL Chi-restraints excluded: chain IC residue 10 VAL Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 3 ASP Chi-restraints excluded: chain ID residue 32 ILE Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 67 VAL Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 42 VAL Chi-restraints excluded: chain JB residue 81 VAL Chi-restraints excluded: chain JC residue 67 VAL Chi-restraints excluded: chain JD residue 42 VAL Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JF residue 42 VAL Chi-restraints excluded: chain KA residue 58 GLU Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KA residue 87 LEU Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KD residue 42 VAL Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 58 GLU Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LE residue 9 GLU Chi-restraints excluded: chain LF residue 32 ILE Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 314 optimal weight: 0.8980 chunk 257 optimal weight: 0.5980 chunk 298 optimal weight: 0.9980 chunk 230 optimal weight: 0.0980 chunk 270 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 349 optimal weight: 0.9980 chunk 320 optimal weight: 0.8980 chunk 192 optimal weight: 0.0070 chunk 323 optimal weight: 0.9980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.091863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.082425 restraints weight = 42423.862| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.82 r_work: 0.2731 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28554 Z= 0.136 Angle : 0.546 6.428 38763 Z= 0.290 Chirality : 0.044 0.209 4668 Planarity : 0.004 0.055 5097 Dihedral : 3.964 19.903 4215 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.93 % Allowed : 13.60 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3837 helix: 0.92 (0.14), residues: 1563 sheet: 1.42 (0.17), residues: 927 loop : -1.67 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARGKC 62 TYR 0.010 0.001 TYRHC 41 PHE 0.009 0.001 PHE A 161 TRP 0.003 0.001 TRP B 102 HIS 0.003 0.001 HISLE 74 Details of bonding type rmsd covalent geometry : bond 0.00325 (28554) covalent geometry : angle 0.54591 (38763) hydrogen bonds : bond 0.03543 ( 1650) hydrogen bonds : angle 3.80987 ( 4803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 614 time to evaluate : 1.693 Fit side-chains REVERT: B 32 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7239 (ptp-110) REVERT: C 58 LYS cc_start: 0.8775 (mtmm) cc_final: 0.8492 (mtmt) REVERT: GA 10 VAL cc_start: 0.9336 (t) cc_final: 0.8987 (m) REVERT: GB 25 LYS cc_start: 0.8430 (mttt) cc_final: 0.8190 (mttt) REVERT: GD 78 ARG cc_start: 0.8512 (mmm160) cc_final: 0.6184 (mtt90) REVERT: GE 8 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8894 (tp) REVERT: GE 41 TYR cc_start: 0.9265 (m-80) cc_final: 0.8696 (m-80) REVERT: HC 3 ASP cc_start: 0.8486 (m-30) cc_final: 0.8133 (m-30) REVERT: HD 78 ARG cc_start: 0.8422 (mmm160) cc_final: 0.6861 (mtt90) REVERT: HE 11 ARG cc_start: 0.8850 (ttt-90) cc_final: 0.8308 (ttt90) REVERT: HE 23 MET cc_start: 0.8798 (mtp) cc_final: 0.8574 (mtp) REVERT: HF 54 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8253 (mttt) REVERT: IA 11 ARG cc_start: 0.8890 (ttm-80) cc_final: 0.8688 (ttt-90) REVERT: IC 28 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8327 (mmtm) REVERT: IE 35 GLU cc_start: 0.8720 (tp30) cc_final: 0.8501 (tp30) REVERT: IF 5 LEU cc_start: 0.9039 (tp) cc_final: 0.8808 (tp) REVERT: JA 28 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8430 (tttp) REVERT: JA 36 LYS cc_start: 0.9289 (mtmm) cc_final: 0.9073 (mtpt) REVERT: JB 36 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8817 (mttt) REVERT: JB 54 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8317 (mtpp) REVERT: JC 58 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7628 (mp0) REVERT: JD 54 LYS cc_start: 0.8646 (tptp) cc_final: 0.8425 (tptt) REVERT: JE 58 GLU cc_start: 0.8267 (pt0) cc_final: 0.7863 (mm-30) REVERT: KA 58 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: KC 28 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8329 (mmtm) REVERT: KC 66 ARG cc_start: 0.8680 (mtp85) cc_final: 0.8260 (mtp-110) REVERT: KD 78 ARG cc_start: 0.8708 (mmm160) cc_final: 0.6592 (mtm180) REVERT: LA 28 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8263 (tttp) REVERT: LB 11 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.8191 (ttm-80) REVERT: LB 58 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: LC 3 ASP cc_start: 0.8441 (m-30) cc_final: 0.8016 (m-30) REVERT: LC 41 TYR cc_start: 0.9280 (m-80) cc_final: 0.9033 (m-80) REVERT: LC 54 LYS cc_start: 0.8464 (tttm) cc_final: 0.8064 (mmtt) REVERT: LC 58 GLU cc_start: 0.8814 (pt0) cc_final: 0.8248 (mt-10) REVERT: LD 78 ARG cc_start: 0.8330 (mmm160) cc_final: 0.6511 (mtm180) REVERT: LE 9 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8755 (tt0) REVERT: LE 66 ARG cc_start: 0.8654 (mtp85) cc_final: 0.8356 (ptm160) REVERT: LE 78 ARG cc_start: 0.8703 (tpp80) cc_final: 0.7452 (ptt180) outliers start: 80 outliers final: 62 residues processed: 668 average time/residue: 0.2282 time to fit residues: 223.0341 Evaluate side-chains 665 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 597 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 67 VAL Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain GF residue 67 VAL Chi-restraints excluded: chain HA residue 10 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 42 VAL Chi-restraints excluded: chain HB residue 67 VAL Chi-restraints excluded: chain HC residue 42 VAL Chi-restraints excluded: chain HC residue 67 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HF residue 54 LYS Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 54 LYS Chi-restraints excluded: chain IA residue 67 VAL Chi-restraints excluded: chain IC residue 10 VAL Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 3 ASP Chi-restraints excluded: chain ID residue 32 ILE Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 67 VAL Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 42 VAL Chi-restraints excluded: chain JB residue 81 VAL Chi-restraints excluded: chain JC residue 67 VAL Chi-restraints excluded: chain JD residue 42 VAL Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JF residue 42 VAL Chi-restraints excluded: chain KA residue 58 GLU Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KD residue 42 VAL Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 58 GLU Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LE residue 9 GLU Chi-restraints excluded: chain LF residue 32 ILE Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 189 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 299 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 311 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 335 optimal weight: 0.4980 chunk 152 optimal weight: 0.7980 chunk 306 optimal weight: 0.6980 chunk 241 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.090573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.081101 restraints weight = 42328.139| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.81 r_work: 0.2698 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28554 Z= 0.173 Angle : 0.572 6.888 38763 Z= 0.302 Chirality : 0.045 0.256 4668 Planarity : 0.004 0.059 5097 Dihedral : 4.023 20.503 4215 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.97 % Allowed : 13.60 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3837 helix: 0.81 (0.14), residues: 1563 sheet: 1.42 (0.17), residues: 927 loop : -1.69 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGKC 62 TYR 0.018 0.002 TYRJC 41 PHE 0.010 0.001 PHE A 161 TRP 0.005 0.001 TRP C 114 HIS 0.003 0.001 HISGB 74 Details of bonding type rmsd covalent geometry : bond 0.00418 (28554) covalent geometry : angle 0.57157 (38763) hydrogen bonds : bond 0.03738 ( 1650) hydrogen bonds : angle 3.87500 ( 4803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 616 time to evaluate : 1.042 Fit side-chains REVERT: B 32 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7135 (ptp-110) REVERT: GA 10 VAL cc_start: 0.9345 (t) cc_final: 0.9004 (m) REVERT: GB 25 LYS cc_start: 0.8365 (mttt) cc_final: 0.8101 (mttt) REVERT: GD 78 ARG cc_start: 0.8480 (mmm160) cc_final: 0.6076 (mtt90) REVERT: GE 8 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8867 (tp) REVERT: GE 41 TYR cc_start: 0.9253 (m-80) cc_final: 0.8597 (m-80) REVERT: HA 54 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8137 (mtmt) REVERT: HB 36 LYS cc_start: 0.8906 (mtmt) cc_final: 0.8677 (mttt) REVERT: HC 3 ASP cc_start: 0.8496 (m-30) cc_final: 0.8154 (m-30) REVERT: HD 34 TYR cc_start: 0.9170 (p90) cc_final: 0.8914 (p90) REVERT: HD 78 ARG cc_start: 0.8452 (mmm160) cc_final: 0.6904 (mtm-85) REVERT: HE 11 ARG cc_start: 0.8866 (ttt-90) cc_final: 0.8264 (ttt90) REVERT: HE 23 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8582 (mtp) REVERT: HF 54 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8225 (mttt) REVERT: IA 11 ARG cc_start: 0.8910 (ttm-80) cc_final: 0.8523 (ttt-90) REVERT: IC 28 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8316 (mmtm) REVERT: IE 35 GLU cc_start: 0.8718 (tp30) cc_final: 0.8500 (tp30) REVERT: IF 5 LEU cc_start: 0.9080 (tp) cc_final: 0.8866 (tp) REVERT: JA 11 ARG cc_start: 0.8822 (ttt-90) cc_final: 0.8337 (ttt-90) REVERT: JA 28 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8449 (tttp) REVERT: JA 36 LYS cc_start: 0.9298 (mtmm) cc_final: 0.9069 (mtpt) REVERT: JB 36 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8813 (mttt) REVERT: JB 54 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8361 (mtpp) REVERT: JD 54 LYS cc_start: 0.8642 (tptp) cc_final: 0.8398 (tptt) REVERT: KA 58 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: KA 65 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8452 (mt-10) REVERT: KC 28 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8294 (mmtm) REVERT: KC 66 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8255 (mtp-110) REVERT: KC 70 VAL cc_start: 0.9034 (t) cc_final: 0.8831 (p) REVERT: KD 78 ARG cc_start: 0.8717 (mmm160) cc_final: 0.6542 (mtm180) REVERT: LA 28 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8269 (tttp) REVERT: LA 58 GLU cc_start: 0.8370 (pt0) cc_final: 0.8100 (tm-30) REVERT: LB 11 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8171 (ttm-80) REVERT: LB 58 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: LC 3 ASP cc_start: 0.8513 (m-30) cc_final: 0.8088 (m-30) REVERT: LC 41 TYR cc_start: 0.9294 (m-80) cc_final: 0.9013 (m-80) REVERT: LC 54 LYS cc_start: 0.8460 (tttm) cc_final: 0.8048 (mmtt) REVERT: LC 58 GLU cc_start: 0.8787 (pt0) cc_final: 0.8212 (mt-10) REVERT: LD 62 ARG cc_start: 0.6947 (ttp-110) cc_final: 0.6706 (tpp80) REVERT: LD 78 ARG cc_start: 0.8329 (mmm160) cc_final: 0.6552 (mtm180) REVERT: LE 9 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8793 (tt0) REVERT: LE 34 TYR cc_start: 0.9187 (p90) cc_final: 0.8864 (p90) REVERT: LE 66 ARG cc_start: 0.8684 (mtp85) cc_final: 0.8367 (ptm160) REVERT: LE 78 ARG cc_start: 0.8709 (tpp80) cc_final: 0.7442 (ptt180) outliers start: 81 outliers final: 65 residues processed: 672 average time/residue: 0.2295 time to fit residues: 226.3111 Evaluate side-chains 683 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 610 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GD residue 3 ASP Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 43 THR Chi-restraints excluded: chain GD residue 67 VAL Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain GF residue 67 VAL Chi-restraints excluded: chain HA residue 10 VAL Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HA residue 54 LYS Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 23 MET Chi-restraints excluded: chain HB residue 42 VAL Chi-restraints excluded: chain HB residue 67 VAL Chi-restraints excluded: chain HC residue 67 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 23 MET Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HF residue 54 LYS Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 54 LYS Chi-restraints excluded: chain IA residue 67 VAL Chi-restraints excluded: chain IC residue 10 VAL Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 3 ASP Chi-restraints excluded: chain ID residue 32 ILE Chi-restraints excluded: chain ID residue 37 THR Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 67 VAL Chi-restraints excluded: chain JA residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 82 ASN Chi-restraints excluded: chain JB residue 42 VAL Chi-restraints excluded: chain JB residue 81 VAL Chi-restraints excluded: chain JC residue 67 VAL Chi-restraints excluded: chain JD residue 42 VAL Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JF residue 42 VAL Chi-restraints excluded: chain KA residue 58 GLU Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KB residue 10 VAL Chi-restraints excluded: chain KB residue 49 ASP Chi-restraints excluded: chain KC residue 10 VAL Chi-restraints excluded: chain KD residue 42 VAL Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KF residue 10 VAL Chi-restraints excluded: chain LB residue 3 ASP Chi-restraints excluded: chain LB residue 58 GLU Chi-restraints excluded: chain LE residue 9 GLU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LF residue 32 ILE Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 247 optimal weight: 0.8980 chunk 376 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 326 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: GF 82 ASN KF 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.087867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.078245 restraints weight = 42949.842| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.83 r_work: 0.2658 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 28554 Z= 0.250 Angle : 0.635 8.175 38763 Z= 0.335 Chirality : 0.048 0.295 4668 Planarity : 0.005 0.058 5097 Dihedral : 4.234 21.647 4215 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.86 % Allowed : 13.68 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3837 helix: 0.48 (0.13), residues: 1563 sheet: 1.40 (0.17), residues: 927 loop : -1.78 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGIC 62 TYR 0.023 0.002 TYRGB 41 PHE 0.012 0.002 PHE C 104 TRP 0.010 0.001 TRP C 114 HIS 0.004 0.001 HISGB 74 Details of bonding type rmsd covalent geometry : bond 0.00605 (28554) covalent geometry : angle 0.63515 (38763) hydrogen bonds : bond 0.04156 ( 1650) hydrogen bonds : angle 4.06499 ( 4803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7351.01 seconds wall clock time: 125 minutes 53.94 seconds (7553.94 seconds total)