Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 11:05:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f92_31495/07_2023/7f92_31495_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f92_31495/07_2023/7f92_31495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f92_31495/07_2023/7f92_31495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f92_31495/07_2023/7f92_31495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f92_31495/07_2023/7f92_31495_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f92_31495/07_2023/7f92_31495_updated.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.006 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 96 5.16 5 C 14628 2.51 5 N 3048 2.21 5 O 3468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "F ARG 33": "NH1" <-> "NH2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H ARG 148": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "I GLU 227": "OE1" <-> "OE2" Residue "J ARG 33": "NH1" <-> "NH2" Residue "J GLU 48": "OE1" <-> "OE2" Residue "J ARG 101": "NH1" <-> "NH2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "J GLU 227": "OE1" <-> "OE2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K GLU 227": "OE1" <-> "OE2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L GLU 227": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 21240 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "C" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "D" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "F" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "J" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "L" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "H" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "I" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "J" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "L" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "J" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "L" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 9.91, per 1000 atoms: 0.47 Number of scatterers: 21240 At special positions: 0 Unit cell: (99.225, 104.625, 173.475, 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 96 16.00 O 3468 8.00 N 3048 7.00 C 14628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.04 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.04 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.04 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.04 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.04 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.04 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.04 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.04 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.04 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.04 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.04 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.04 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.04 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.04 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.87 Conformation dependent library (CDL) restraints added in 2.6 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 12 sheets defined 62.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 removed outlier: 3.536A pdb=" N ASP A 12 " --> pdb=" O GLY A 8 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 39 removed outlier: 3.544A pdb=" N LEU A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 29 " --> pdb=" O TRP A 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.564A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 69 " --> pdb=" O CYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 104 removed outlier: 3.504A pdb=" N VAL A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.556A pdb=" N PHE A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 176 removed outlier: 3.549A pdb=" N SER A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 232 removed outlier: 3.528A pdb=" N PHE A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.538A pdb=" N ASP B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 39 removed outlier: 3.555A pdb=" N LEU B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 29 " --> pdb=" O TRP B 25 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 44 No H-bonds generated for 'chain 'B' and resid 41 through 44' Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.569A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 104 removed outlier: 3.512A pdb=" N VAL B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.560A pdb=" N PHE B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 176 removed outlier: 3.550A pdb=" N SER B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 232 removed outlier: 3.539A pdb=" N PHE B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 14 removed outlier: 3.537A pdb=" N ASP C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 39 removed outlier: 3.548A pdb=" N LEU C 26 " --> pdb=" O GLY C 22 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 27 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 29 " --> pdb=" O TRP C 25 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 44 No H-bonds generated for 'chain 'C' and resid 41 through 44' Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.554A pdb=" N ASP C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 104 removed outlier: 3.521A pdb=" N VAL C 79 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 3.554A pdb=" N PHE C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 103 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 176 removed outlier: 3.548A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 232 removed outlier: 3.541A pdb=" N PHE C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 217 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 14 removed outlier: 3.537A pdb=" N ASP D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 39 removed outlier: 3.543A pdb=" N LEU D 26 " --> pdb=" O GLY D 22 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER D 27 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 29 " --> pdb=" O TRP D 25 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.563A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 69 " --> pdb=" O CYS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 104 removed outlier: 3.504A pdb=" N VAL D 79 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Proline residue: D 88 - end of helix removed outlier: 3.556A pdb=" N PHE D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 176 removed outlier: 3.550A pdb=" N SER D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 232 removed outlier: 3.526A pdb=" N PHE D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 217 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 14 removed outlier: 3.538A pdb=" N ASP E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 39 removed outlier: 3.555A pdb=" N LEU E 26 " --> pdb=" O GLY E 22 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 29 " --> pdb=" O TRP E 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 44 No H-bonds generated for 'chain 'E' and resid 41 through 44' Processing helix chain 'E' and resid 61 through 69 removed outlier: 3.569A pdb=" N ASP E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER E 69 " --> pdb=" O CYS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 104 removed outlier: 3.512A pdb=" N VAL E 79 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 80 " --> pdb=" O ARG E 76 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 3.561A pdb=" N PHE E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU E 103 " --> pdb=" O VAL E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 176 removed outlier: 3.549A pdb=" N SER E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 163 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 166 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN E 173 " --> pdb=" O PHE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 232 removed outlier: 3.537A pdb=" N PHE E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 217 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN E 224 " --> pdb=" O SER E 220 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 14 removed outlier: 3.536A pdb=" N ASP F 12 " --> pdb=" O GLY F 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 39 removed outlier: 3.547A pdb=" N LEU F 26 " --> pdb=" O GLY F 22 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 29 " --> pdb=" O TRP F 25 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE F 31 " --> pdb=" O SER F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 44 No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 61 through 69 removed outlier: 3.555A pdb=" N ASP F 67 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 104 removed outlier: 3.521A pdb=" N VAL F 79 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 80 " --> pdb=" O ARG F 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER F 86 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Proline residue: F 88 - end of helix removed outlier: 3.553A pdb=" N PHE F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 176 removed outlier: 3.548A pdb=" N SER F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU F 166 " --> pdb=" O LYS F 162 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 170 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN F 173 " --> pdb=" O PHE F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 232 removed outlier: 3.544A pdb=" N PHE F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER F 217 " --> pdb=" O MET F 213 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 14 removed outlier: 3.538A pdb=" N ASP G 12 " --> pdb=" O GLY G 8 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 39 removed outlier: 3.547A pdb=" N LEU G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU G 29 " --> pdb=" O TRP G 25 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE G 30 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 44 No H-bonds generated for 'chain 'G' and resid 41 through 44' Processing helix chain 'G' and resid 61 through 69 removed outlier: 3.555A pdb=" N ASP G 67 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER G 69 " --> pdb=" O CYS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 104 removed outlier: 3.521A pdb=" N VAL G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 80 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER G 86 " --> pdb=" O ILE G 82 " (cutoff:3.500A) Proline residue: G 88 - end of helix removed outlier: 3.554A pdb=" N PHE G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU G 103 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 176 removed outlier: 3.546A pdb=" N SER G 158 " --> pdb=" O THR G 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 163 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU G 166 " --> pdb=" O LYS G 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 170 " --> pdb=" O GLU G 166 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN G 173 " --> pdb=" O PHE G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 232 removed outlier: 3.541A pdb=" N PHE G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G 227 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 14 removed outlier: 3.536A pdb=" N ASP H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 39 removed outlier: 3.544A pdb=" N LEU H 26 " --> pdb=" O GLY H 22 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU H 29 " --> pdb=" O TRP H 25 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE H 31 " --> pdb=" O SER H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 44 No H-bonds generated for 'chain 'H' and resid 41 through 44' Processing helix chain 'H' and resid 61 through 69 removed outlier: 3.564A pdb=" N ASP H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER H 69 " --> pdb=" O CYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 104 removed outlier: 3.503A pdb=" N VAL H 79 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER H 86 " --> pdb=" O ILE H 82 " (cutoff:3.500A) Proline residue: H 88 - end of helix removed outlier: 3.556A pdb=" N PHE H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 176 removed outlier: 3.551A pdb=" N SER H 158 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU H 166 " --> pdb=" O LYS H 162 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 172 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN H 173 " --> pdb=" O PHE H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 232 removed outlier: 3.526A pdb=" N PHE H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER H 217 " --> pdb=" O MET H 213 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN H 224 " --> pdb=" O SER H 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE H 226 " --> pdb=" O ALA H 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU H 227 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 14 removed outlier: 3.538A pdb=" N ASP I 12 " --> pdb=" O GLY I 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 39 removed outlier: 3.554A pdb=" N LEU I 26 " --> pdb=" O GLY I 22 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU I 29 " --> pdb=" O TRP I 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE I 30 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 44 No H-bonds generated for 'chain 'I' and resid 41 through 44' Processing helix chain 'I' and resid 61 through 69 removed outlier: 3.568A pdb=" N ASP I 67 " --> pdb=" O ASN I 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER I 69 " --> pdb=" O CYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 104 removed outlier: 3.513A pdb=" N VAL I 79 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU I 80 " --> pdb=" O ARG I 76 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 84 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER I 86 " --> pdb=" O ILE I 82 " (cutoff:3.500A) Proline residue: I 88 - end of helix removed outlier: 3.561A pdb=" N PHE I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU I 103 " --> pdb=" O VAL I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 176 removed outlier: 3.549A pdb=" N SER I 158 " --> pdb=" O THR I 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER I 163 " --> pdb=" O ILE I 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE I 172 " --> pdb=" O ALA I 168 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN I 173 " --> pdb=" O PHE I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 232 removed outlier: 3.540A pdb=" N PHE I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER I 217 " --> pdb=" O MET I 213 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN I 224 " --> pdb=" O SER I 220 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU I 227 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 231 " --> pdb=" O GLU I 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 14 removed outlier: 3.536A pdb=" N ASP J 12 " --> pdb=" O GLY J 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 39 removed outlier: 3.548A pdb=" N LEU J 26 " --> pdb=" O GLY J 22 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER J 27 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU J 29 " --> pdb=" O TRP J 25 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE J 30 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE J 31 " --> pdb=" O SER J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 44 No H-bonds generated for 'chain 'J' and resid 41 through 44' Processing helix chain 'J' and resid 61 through 69 removed outlier: 3.555A pdb=" N ASP J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER J 69 " --> pdb=" O CYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 104 removed outlier: 3.521A pdb=" N VAL J 79 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU J 80 " --> pdb=" O ARG J 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER J 86 " --> pdb=" O ILE J 82 " (cutoff:3.500A) Proline residue: J 88 - end of helix removed outlier: 3.554A pdb=" N PHE J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR J 98 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU J 103 " --> pdb=" O VAL J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 176 removed outlier: 3.547A pdb=" N SER J 158 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER J 163 " --> pdb=" O ILE J 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU J 166 " --> pdb=" O LYS J 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 170 " --> pdb=" O GLU J 166 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE J 172 " --> pdb=" O ALA J 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN J 173 " --> pdb=" O PHE J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 232 removed outlier: 3.542A pdb=" N PHE J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER J 217 " --> pdb=" O MET J 213 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN J 224 " --> pdb=" O SER J 220 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE J 226 " --> pdb=" O ALA J 222 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL J 231 " --> pdb=" O GLU J 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 14 removed outlier: 3.536A pdb=" N ASP K 12 " --> pdb=" O GLY K 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL K 14 " --> pdb=" O LEU K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 39 removed outlier: 3.544A pdb=" N LEU K 26 " --> pdb=" O GLY K 22 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER K 27 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU K 29 " --> pdb=" O TRP K 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE K 31 " --> pdb=" O SER K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 44 No H-bonds generated for 'chain 'K' and resid 41 through 44' Processing helix chain 'K' and resid 61 through 69 removed outlier: 3.564A pdb=" N ASP K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER K 69 " --> pdb=" O CYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 104 removed outlier: 3.504A pdb=" N VAL K 79 " --> pdb=" O VAL K 75 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU K 80 " --> pdb=" O ARG K 76 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE K 84 " --> pdb=" O LEU K 80 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) Proline residue: K 88 - end of helix removed outlier: 3.555A pdb=" N PHE K 97 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR K 98 " --> pdb=" O ALA K 94 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU K 103 " --> pdb=" O VAL K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 176 removed outlier: 3.550A pdb=" N SER K 158 " --> pdb=" O THR K 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER K 163 " --> pdb=" O ILE K 159 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 172 " --> pdb=" O ALA K 168 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN K 173 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 232 removed outlier: 3.526A pdb=" N PHE K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER K 217 " --> pdb=" O MET K 213 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN K 224 " --> pdb=" O SER K 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE K 226 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU K 227 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 14 removed outlier: 3.539A pdb=" N ASP L 12 " --> pdb=" O GLY L 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 39 removed outlier: 3.555A pdb=" N LEU L 26 " --> pdb=" O GLY L 22 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER L 27 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU L 29 " --> pdb=" O TRP L 25 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE L 30 " --> pdb=" O LEU L 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE L 31 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 44 No H-bonds generated for 'chain 'L' and resid 41 through 44' Processing helix chain 'L' and resid 61 through 69 removed outlier: 3.569A pdb=" N ASP L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER L 69 " --> pdb=" O CYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 104 removed outlier: 3.513A pdb=" N VAL L 79 " --> pdb=" O VAL L 75 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU L 80 " --> pdb=" O ARG L 76 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE L 84 " --> pdb=" O LEU L 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER L 86 " --> pdb=" O ILE L 82 " (cutoff:3.500A) Proline residue: L 88 - end of helix removed outlier: 3.561A pdb=" N PHE L 97 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU L 103 " --> pdb=" O VAL L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 176 removed outlier: 3.549A pdb=" N SER L 158 " --> pdb=" O THR L 154 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER L 163 " --> pdb=" O ILE L 159 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU L 166 " --> pdb=" O LYS L 162 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN L 173 " --> pdb=" O PHE L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 232 removed outlier: 3.539A pdb=" N PHE L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER L 217 " --> pdb=" O MET L 213 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE L 226 " --> pdb=" O ALA L 222 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU L 227 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL L 231 " --> pdb=" O GLU L 227 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 184 through 187 Processing sheet with id= B, first strand: chain 'B' and resid 184 through 187 Processing sheet with id= C, first strand: chain 'C' and resid 184 through 187 Processing sheet with id= D, first strand: chain 'D' and resid 184 through 187 Processing sheet with id= E, first strand: chain 'E' and resid 184 through 187 Processing sheet with id= F, first strand: chain 'F' and resid 184 through 187 Processing sheet with id= G, first strand: chain 'G' and resid 184 through 187 Processing sheet with id= H, first strand: chain 'H' and resid 184 through 187 Processing sheet with id= I, first strand: chain 'I' and resid 184 through 187 Processing sheet with id= J, first strand: chain 'J' and resid 184 through 187 Processing sheet with id= K, first strand: chain 'K' and resid 184 through 187 Processing sheet with id= L, first strand: chain 'L' and resid 184 through 187 812 hydrogen bonds defined for protein. 2400 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: 5.08 Time building geometry restraints manager: 7.48 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: 5531 1.34 - 1.46: 4578 1.46 - 1.58: 11131 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 21360 Sorted by residual: bond pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 1.99e+00 bond pdb=" C VAL J 87 " pdb=" N PRO J 88 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.25e-02 6.40e+03 1.91e+00 bond pdb=" C VAL G 87 " pdb=" N PRO G 88 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.25e-02 6.40e+03 1.91e+00 bond pdb=" C VAL F 87 " pdb=" N PRO F 88 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.25e-02 6.40e+03 1.90e+00 bond pdb=" C VAL K 87 " pdb=" N PRO K 88 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.25e-02 6.40e+03 1.84e+00 ... (remaining 21355 not shown) Histogram of bond angle deviations from ideal: 101.21 - 107.94: 749 107.94 - 114.68: 12699 114.68 - 121.42: 10225 121.42 - 128.15: 4319 128.15 - 134.89: 208 Bond angle restraints: 28200 Sorted by residual: angle pdb=" C ASP C 190 " pdb=" N PRO C 191 " pdb=" CA PRO C 191 " ideal model delta sigma weight residual 127.00 134.89 -7.89 2.40e+00 1.74e-01 1.08e+01 angle pdb=" C ASP J 190 " pdb=" N PRO J 191 " pdb=" CA PRO J 191 " ideal model delta sigma weight residual 127.00 134.85 -7.85 2.40e+00 1.74e-01 1.07e+01 angle pdb=" C ASP F 190 " pdb=" N PRO F 191 " pdb=" CA PRO F 191 " ideal model delta sigma weight residual 127.00 134.83 -7.83 2.40e+00 1.74e-01 1.06e+01 angle pdb=" C ASP G 190 " pdb=" N PRO G 191 " pdb=" CA PRO G 191 " ideal model delta sigma weight residual 127.00 134.81 -7.81 2.40e+00 1.74e-01 1.06e+01 angle pdb=" C ASP B 190 " pdb=" N PRO B 191 " pdb=" CA PRO B 191 " ideal model delta sigma weight residual 127.00 134.73 -7.73 2.40e+00 1.74e-01 1.04e+01 ... (remaining 28195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 11018 17.30 - 34.60: 1390 34.60 - 51.89: 396 51.89 - 69.19: 108 69.19 - 86.49: 12 Dihedral angle restraints: 12924 sinusoidal: 6048 harmonic: 6876 Sorted by residual: dihedral pdb=" CB CYS J 61 " pdb=" SG CYS J 61 " pdb=" SG CYS J 192 " pdb=" CB CYS J 192 " ideal model delta sinusoidal sigma weight residual 93.00 125.52 -32.52 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS H 61 " pdb=" SG CYS H 61 " pdb=" SG CYS H 192 " pdb=" CB CYS H 192 " ideal model delta sinusoidal sigma weight residual 93.00 125.50 -32.50 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CB CYS C 61 " pdb=" SG CYS C 61 " pdb=" SG CYS C 192 " pdb=" CB CYS C 192 " ideal model delta sinusoidal sigma weight residual 93.00 125.49 -32.49 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 12921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1992 0.049 - 0.097: 936 0.097 - 0.146: 54 0.146 - 0.194: 30 0.194 - 0.243: 12 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CB VAL G 41 " pdb=" CA VAL G 41 " pdb=" CG1 VAL G 41 " pdb=" CG2 VAL G 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL F 41 " pdb=" CA VAL F 41 " pdb=" CG1 VAL F 41 " pdb=" CG2 VAL F 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL E 41 " pdb=" CA VAL E 41 " pdb=" CG1 VAL E 41 " pdb=" CG2 VAL E 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3021 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L 58 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO L 59 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 58 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO A 59 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 58 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO D 59 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " -0.025 5.00e-02 4.00e+02 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5535 2.80 - 3.32: 14534 3.32 - 3.85: 30146 3.85 - 4.37: 37464 4.37 - 4.90: 66874 Nonbonded interactions: 154553 Sorted by model distance: nonbonded pdb=" O ILE I 72 " pdb=" OH TYR I 177 " model vdw 2.271 2.440 nonbonded pdb=" O ILE L 72 " pdb=" OH TYR L 177 " model vdw 2.272 2.440 nonbonded pdb=" O ILE E 72 " pdb=" OH TYR E 177 " model vdw 2.273 2.440 nonbonded pdb=" O ILE B 72 " pdb=" OH TYR B 177 " model vdw 2.273 2.440 nonbonded pdb=" O ILE J 72 " pdb=" OH TYR J 177 " model vdw 2.274 2.440 ... (remaining 154548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.610 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: 0.010 Extract box with map and model: 13.510 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 46.420 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.180 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 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 : 0.008 0.064 21360 Z= 0.507 Angle : 1.289 8.177 28200 Z= 0.553 Chirality : 0.050 0.243 3024 Planarity : 0.006 0.046 3204 Dihedral : 16.753 86.487 8376 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.40 (0.11), residues: 2304 helix: -4.78 (0.04), residues: 1536 sheet: 0.21 (0.39), residues: 204 loop : -3.37 (0.20), residues: 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 2.086 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 232 average time/residue: 0.4535 time to fit residues: 146.6623 Evaluate side-chains 200 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3409 time to fit residues: 15.0334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 172 optimal weight: 0.0570 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 178 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 49 GLN C 49 GLN D 49 GLN E 49 GLN F 49 GLN G 49 GLN H 49 GLN I 49 GLN J 49 GLN K 49 GLN L 49 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 21360 Z= 0.122 Angle : 0.470 4.828 28200 Z= 0.246 Chirality : 0.034 0.099 3024 Planarity : 0.004 0.028 3204 Dihedral : 10.664 58.492 3984 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.14), residues: 2304 helix: -2.35 (0.10), residues: 1464 sheet: 0.56 (0.39), residues: 204 loop : -2.84 (0.20), residues: 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 2.088 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 172 average time/residue: 0.4434 time to fit residues: 107.9566 Evaluate side-chains 156 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 21360 Z= 0.283 Angle : 0.573 4.892 28200 Z= 0.288 Chirality : 0.039 0.124 3024 Planarity : 0.004 0.033 3204 Dihedral : 10.975 51.381 3984 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2304 helix: -0.97 (0.13), residues: 1464 sheet: 0.81 (0.39), residues: 204 loop : -2.45 (0.21), residues: 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 2.168 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 200 average time/residue: 0.4262 time to fit residues: 121.8184 Evaluate side-chains 180 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 2.170 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1972 time to fit residues: 10.2185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.0570 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 208 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 21360 Z= 0.110 Angle : 0.418 4.779 28200 Z= 0.211 Chirality : 0.034 0.100 3024 Planarity : 0.003 0.025 3204 Dihedral : 8.733 48.912 3984 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2304 helix: -0.04 (0.13), residues: 1464 sheet: 1.13 (0.41), residues: 204 loop : -2.27 (0.21), residues: 636 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 2.100 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 196 average time/residue: 0.4200 time to fit residues: 118.2635 Evaluate side-chains 160 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 2.056 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1754 time to fit residues: 6.8256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 197 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 21360 Z= 0.131 Angle : 0.438 4.806 28200 Z= 0.220 Chirality : 0.035 0.105 3024 Planarity : 0.003 0.024 3204 Dihedral : 8.618 47.274 3984 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2304 helix: 0.49 (0.13), residues: 1464 sheet: 1.16 (0.41), residues: 204 loop : -2.03 (0.21), residues: 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 2.284 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 156 average time/residue: 0.4607 time to fit residues: 101.8666 Evaluate side-chains 152 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 21360 Z= 0.123 Angle : 0.423 4.770 28200 Z= 0.213 Chirality : 0.035 0.103 3024 Planarity : 0.002 0.023 3204 Dihedral : 8.303 45.349 3984 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2304 helix: 0.93 (0.13), residues: 1464 sheet: 1.23 (0.41), residues: 204 loop : -1.81 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 2.039 Fit side-chains outliers start: 17 outliers final: 4 residues processed: 164 average time/residue: 0.4672 time to fit residues: 105.8452 Evaluate side-chains 156 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 2.086 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2174 time to fit residues: 4.5876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 0.0170 chunk 123 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 21360 Z= 0.199 Angle : 0.491 4.780 28200 Z= 0.246 Chirality : 0.037 0.116 3024 Planarity : 0.003 0.025 3204 Dihedral : 9.228 45.996 3984 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2304 helix: 0.92 (0.13), residues: 1476 sheet: 1.10 (0.40), residues: 204 loop : -1.79 (0.22), residues: 624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 2.296 Fit side-chains outliers start: 33 outliers final: 5 residues processed: 200 average time/residue: 0.4437 time to fit residues: 126.1324 Evaluate side-chains 169 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 2.163 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2125 time to fit residues: 4.8508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 139 optimal weight: 0.3980 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 21360 Z= 0.231 Angle : 0.528 5.158 28200 Z= 0.262 Chirality : 0.038 0.119 3024 Planarity : 0.003 0.027 3204 Dihedral : 9.721 47.660 3984 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2304 helix: 0.90 (0.13), residues: 1464 sheet: 0.99 (0.39), residues: 204 loop : -1.63 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 2.318 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 178 average time/residue: 0.4549 time to fit residues: 114.2142 Evaluate side-chains 165 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 2.148 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1847 time to fit residues: 7.3903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 10.0000 chunk 210 optimal weight: 0.0980 chunk 192 optimal weight: 0.9990 chunk 204 optimal weight: 0.1980 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 21360 Z= 0.102 Angle : 0.420 4.709 28200 Z= 0.209 Chirality : 0.034 0.098 3024 Planarity : 0.002 0.024 3204 Dihedral : 8.263 44.379 3984 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2304 helix: 1.35 (0.13), residues: 1464 sheet: 1.10 (0.40), residues: 204 loop : -1.50 (0.23), residues: 636 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 2.196 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 158 average time/residue: 0.4692 time to fit residues: 105.1179 Evaluate side-chains 151 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5402 time to fit residues: 3.8164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 21360 Z= 0.117 Angle : 0.437 4.744 28200 Z= 0.217 Chirality : 0.035 0.101 3024 Planarity : 0.002 0.022 3204 Dihedral : 8.048 42.253 3984 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2304 helix: 1.57 (0.13), residues: 1476 sheet: 1.07 (0.40), residues: 204 loop : -1.52 (0.23), residues: 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 2.177 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 155 average time/residue: 0.4498 time to fit residues: 99.8175 Evaluate side-chains 153 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1821 time to fit residues: 4.1543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 159 optimal weight: 0.1980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 HIS F 95 HIS G 95 HIS J 95 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.146122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109391 restraints weight = 21603.206| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.16 r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.016 21360 Z= 0.091 Angle : 0.405 4.729 28200 Z= 0.200 Chirality : 0.034 0.099 3024 Planarity : 0.002 0.017 3204 Dihedral : 7.228 37.121 3984 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.18), residues: 2304 helix: 1.94 (0.13), residues: 1476 sheet: 1.12 (0.41), residues: 204 loop : -1.44 (0.24), residues: 624 =============================================================================== Job complete usr+sys time: 3979.41 seconds wall clock time: 73 minutes 7.07 seconds (4387.07 seconds total)