Starting phenix.real_space_refine on Sun Feb 18 04:00:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/02_2024/7f93_31496_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/02_2024/7f93_31496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/02_2024/7f93_31496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/02_2024/7f93_31496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/02_2024/7f93_31496_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/02_2024/7f93_31496_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.047 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 14460 2.51 5 N 3048 2.21 5 O 3204 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 42": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "F ARG 33": "NH1" <-> "NH2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I GLU 103": "OE1" <-> "OE2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I GLU 227": "OE1" <-> "OE2" Residue "J ARG 33": "NH1" <-> "NH2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 48": "OE1" <-> "OE2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J ARG 101": "NH1" <-> "NH2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J GLU 227": "OE1" <-> "OE2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K GLU 227": "OE1" <-> "OE2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "L GLU 227": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20808 Number of models: 1 Model: "" Number of chains: 24 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'C14': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'C14': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 10.48, per 1000 atoms: 0.50 Number of scatterers: 20808 At special positions: 0 Unit cell: (97.8945, 103.13, 172.232, 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 3204 8.00 N 3048 7.00 C 14460 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 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=2.03 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: 7.37 Conformation dependent library (CDL) restraints added in 3.1 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: 72 helices and 12 sheets defined 62.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 69 " --> pdb=" O CYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 104 removed outlier: 3.746A pdb=" N PHE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.584A pdb=" N TYR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 176 removed outlier: 3.562A pdb=" N ILE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 233 removed outlier: 3.690A pdb=" N PHE A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 104 removed outlier: 3.746A pdb=" N PHE B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.583A pdb=" N TYR B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 176 removed outlier: 3.561A pdb=" N ILE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 233 removed outlier: 3.689A pdb=" N PHE B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER C 27 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 104 removed outlier: 3.746A pdb=" N PHE C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 3.583A pdb=" N TYR C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 176 removed outlier: 3.561A pdb=" N ILE C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 233 removed outlier: 3.688A pdb=" N PHE C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 217 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS D 9 " --> pdb=" O SER D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER D 27 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL D 28 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 68 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 69 " --> pdb=" O CYS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 104 removed outlier: 3.747A pdb=" N PHE D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Proline residue: D 88 - end of helix removed outlier: 3.583A pdb=" N TYR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 176 removed outlier: 3.560A pdb=" N ILE D 159 " --> pdb=" O TYR D 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 233 removed outlier: 3.688A pdb=" N PHE D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 217 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 39 removed outlier: 4.108A pdb=" N SER E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 69 removed outlier: 3.764A pdb=" N ASP E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER E 69 " --> pdb=" O CYS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 104 removed outlier: 3.746A pdb=" N PHE E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 3.584A pdb=" N TYR E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 176 removed outlier: 3.561A pdb=" N ILE E 159 " --> pdb=" O TYR E 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN E 173 " --> pdb=" O PHE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 233 removed outlier: 3.688A pdb=" N PHE E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 217 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL F 28 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR F 39 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP F 67 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS F 68 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 104 removed outlier: 3.746A pdb=" N PHE F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Proline residue: F 88 - end of helix removed outlier: 3.583A pdb=" N TYR F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 176 removed outlier: 3.560A pdb=" N ILE F 159 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN F 173 " --> pdb=" O PHE F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 233 removed outlier: 3.689A pdb=" N PHE F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER F 217 " --> pdb=" O MET F 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 13 removed outlier: 3.729A pdb=" N LYS G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR G 39 " --> pdb=" O LEU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP G 67 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 69 " --> pdb=" O CYS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 104 removed outlier: 3.746A pdb=" N PHE G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Proline residue: G 88 - end of helix removed outlier: 3.584A pdb=" N TYR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 176 removed outlier: 3.562A pdb=" N ILE G 159 " --> pdb=" O TYR G 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN G 173 " --> pdb=" O PHE G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 233 removed outlier: 3.689A pdb=" N PHE G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU G 227 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL H 28 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 69 " --> pdb=" O CYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 104 removed outlier: 3.747A pdb=" N PHE H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Proline residue: H 88 - end of helix removed outlier: 3.584A pdb=" N TYR H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 176 removed outlier: 3.561A pdb=" N ILE H 159 " --> pdb=" O TYR H 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE H 172 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN H 173 " --> pdb=" O PHE H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 233 removed outlier: 3.690A pdb=" N PHE H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER H 217 " --> pdb=" O MET H 213 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU H 227 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL I 28 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR I 39 " --> pdb=" O LEU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP I 67 " --> pdb=" O ASN I 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER I 69 " --> pdb=" O CYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 104 removed outlier: 3.747A pdb=" N PHE I 84 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Proline residue: I 88 - end of helix removed outlier: 3.584A pdb=" N TYR I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 176 removed outlier: 3.560A pdb=" N ILE I 159 " --> pdb=" O TYR I 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS I 162 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE I 172 " --> pdb=" O ALA I 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN I 173 " --> pdb=" O PHE I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 233 removed outlier: 3.688A pdb=" N PHE I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER I 217 " --> pdb=" O MET I 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU I 227 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER J 27 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL J 28 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 69 removed outlier: 3.764A pdb=" N ASP J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS J 68 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER J 69 " --> pdb=" O CYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 104 removed outlier: 3.747A pdb=" N PHE J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Proline residue: J 88 - end of helix removed outlier: 3.584A pdb=" N TYR J 98 " --> pdb=" O ALA J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 176 removed outlier: 3.560A pdb=" N ILE J 159 " --> pdb=" O TYR J 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS J 162 " --> pdb=" O SER J 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE J 172 " --> pdb=" O ALA J 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 173 " --> pdb=" O PHE J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 233 removed outlier: 3.689A pdb=" N PHE J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER J 217 " --> pdb=" O MET J 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 39 removed outlier: 4.107A pdb=" N SER K 27 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL K 28 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR K 39 " --> pdb=" O LEU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS K 68 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER K 69 " --> pdb=" O CYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 104 removed outlier: 3.747A pdb=" N PHE K 84 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Proline residue: K 88 - end of helix removed outlier: 3.582A pdb=" N TYR K 98 " --> pdb=" O ALA K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 176 removed outlier: 3.561A pdb=" N ILE K 159 " --> pdb=" O TYR K 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS K 162 " --> pdb=" O SER K 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE K 172 " --> pdb=" O ALA K 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN K 173 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 233 removed outlier: 3.689A pdb=" N PHE K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER K 217 " --> pdb=" O MET K 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU K 227 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 13 removed outlier: 3.728A pdb=" N LYS L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 39 removed outlier: 4.108A pdb=" N SER L 27 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL L 28 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR L 39 " --> pdb=" O LEU L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 69 removed outlier: 3.763A pdb=" N ASP L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER L 69 " --> pdb=" O CYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 104 removed outlier: 3.748A pdb=" N PHE L 84 " --> pdb=" O LEU L 80 " (cutoff:3.500A) Proline residue: L 88 - end of helix removed outlier: 3.583A pdb=" N TYR L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 176 removed outlier: 3.560A pdb=" N ILE L 159 " --> pdb=" O TYR L 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS L 162 " --> pdb=" O SER L 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN L 173 " --> pdb=" O PHE L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 233 removed outlier: 3.688A pdb=" N PHE L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER L 217 " --> pdb=" O MET L 213 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU L 227 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE L 232 " --> pdb=" O LEU L 228 " (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 187 996 hydrogen bonds defined for protein. 2952 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: 5.53 Time building geometry restraints manager: 7.96 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: 5590 1.34 - 1.46: 4875 1.46 - 1.58: 10619 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 21204 Sorted by residual: bond pdb=" C VAL L 87 " pdb=" N PRO L 88 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.25e-02 6.40e+03 3.60e+00 bond pdb=" C VAL J 87 " pdb=" N PRO J 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.58e+00 bond pdb=" C VAL E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.57e+00 bond pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.52e+00 bond pdb=" C VAL A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.49e+00 ... (remaining 21199 not shown) Histogram of bond angle deviations from ideal: 100.04 - 107.29: 523 107.29 - 114.53: 12913 114.53 - 121.78: 11150 121.78 - 129.02: 3290 129.02 - 136.27: 180 Bond angle restraints: 28056 Sorted by residual: angle pdb=" CA PRO D 88 " pdb=" N PRO D 88 " pdb=" CD PRO D 88 " ideal model delta sigma weight residual 112.00 107.10 4.90 1.40e+00 5.10e-01 1.22e+01 angle pdb=" CA PRO K 88 " pdb=" N PRO K 88 " pdb=" CD PRO K 88 " ideal model delta sigma weight residual 112.00 107.13 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 112.00 107.13 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" CA PRO J 88 " pdb=" N PRO J 88 " pdb=" CD PRO J 88 " ideal model delta sigma weight residual 112.00 107.14 4.86 1.40e+00 5.10e-01 1.21e+01 angle pdb=" CA PRO H 88 " pdb=" N PRO H 88 " pdb=" CD PRO H 88 " ideal model delta sigma weight residual 112.00 107.14 4.86 1.40e+00 5.10e-01 1.20e+01 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 10630 16.56 - 33.11: 1538 33.11 - 49.67: 492 49.67 - 66.22: 96 66.22 - 82.78: 36 Dihedral angle restraints: 12792 sinusoidal: 5916 harmonic: 6876 Sorted by residual: dihedral pdb=" C VAL K 87 " pdb=" N VAL K 87 " pdb=" CA VAL K 87 " pdb=" CB VAL K 87 " ideal model delta harmonic sigma weight residual -122.00 -130.32 8.32 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" C VAL E 87 " pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" CB VAL E 87 " ideal model delta harmonic sigma weight residual -122.00 -130.31 8.31 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C VAL F 87 " pdb=" N VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta harmonic sigma weight residual -122.00 -130.28 8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 12789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2168 0.049 - 0.099: 729 0.099 - 0.148: 103 0.148 - 0.198: 7 0.198 - 0.247: 17 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CB VAL F 87 " pdb=" CA VAL F 87 " pdb=" CG1 VAL F 87 " pdb=" CG2 VAL F 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL B 87 " pdb=" CA VAL B 87 " pdb=" CG1 VAL B 87 " pdb=" CG2 VAL B 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB VAL C 87 " pdb=" CA VAL C 87 " pdb=" CG1 VAL C 87 " pdb=" CG2 VAL C 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3021 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS H 192 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO H 193 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 193 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 193 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS F 192 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO F 193 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 193 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 192 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.02e+00 pdb=" N PRO A 193 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.028 5.00e-02 4.00e+02 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6218 2.81 - 3.34: 16693 3.34 - 3.86: 31260 3.86 - 4.38: 34561 4.38 - 4.90: 61045 Nonbonded interactions: 149777 Sorted by model distance: nonbonded pdb=" O PRO A 203 " pdb=" OG1 THR A 207 " model vdw 2.293 2.440 nonbonded pdb=" O PRO G 203 " pdb=" OG1 THR G 207 " model vdw 2.293 2.440 nonbonded pdb=" O PRO F 203 " pdb=" OG1 THR F 207 " model vdw 2.293 2.440 nonbonded pdb=" O PRO K 203 " pdb=" OG1 THR K 207 " model vdw 2.293 2.440 nonbonded pdb=" O PRO C 203 " pdb=" OG1 THR C 207 " model vdw 2.293 2.440 ... (remaining 149772 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' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'B' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'C' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'D' and (resid 2 through 235 or resid 401 through 409)) selection = chain 'E' selection = (chain 'F' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'G' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'H' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'I' and (resid 2 through 235 or resid 401 through 409)) selection = (chain 'J' and (resid 2 through 235 or resid 401 through 409)) selection = chain 'K' selection = (chain 'L' and (resid 2 through 235 or resid 401 through 409)) } 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 group one per residue 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: 7.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 28.430 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 51.090 Find NCS groups from input model: 1.500 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 21204 Z= 0.461 Angle : 1.261 11.268 28056 Z= 0.576 Chirality : 0.050 0.247 3024 Planarity : 0.006 0.051 3204 Dihedral : 16.993 82.776 8244 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.00 % Allowed : 10.29 % Favored : 85.71 % 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: -5.48 (0.11), residues: 2304 helix: -3.98 (0.05), residues: 1548 sheet: 1.37 (0.48), residues: 132 loop : -3.13 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 45 HIS 0.004 0.001 HIS H 95 PHE 0.020 0.002 PHE F 52 TYR 0.008 0.002 TYR A 155 ARG 0.002 0.000 ARG K 33 *********************** 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 636 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 552 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7816 (t0) cc_final: 0.7502 (t70) REVERT: A 47 ASP cc_start: 0.9174 (p0) cc_final: 0.8857 (p0) REVERT: A 82 ILE cc_start: 0.8793 (tt) cc_final: 0.8593 (tp) REVERT: A 185 TYR cc_start: 0.9025 (t80) cc_final: 0.8666 (t80) REVERT: A 213 MET cc_start: 0.8445 (mmm) cc_final: 0.7182 (mmm) REVERT: B 3 ASP cc_start: 0.7643 (t0) cc_final: 0.7186 (t70) REVERT: B 42 GLU cc_start: 0.7786 (tp30) cc_final: 0.7579 (tp30) REVERT: B 55 ASN cc_start: 0.9229 (t0) cc_final: 0.8792 (t0) REVERT: B 206 LYS cc_start: 0.9157 (mttt) cc_final: 0.8490 (mttp) REVERT: C 55 ASN cc_start: 0.9171 (t0) cc_final: 0.8957 (t0) REVERT: D 3 ASP cc_start: 0.7910 (t0) cc_final: 0.7571 (t70) REVERT: D 42 GLU cc_start: 0.7924 (tp30) cc_final: 0.7612 (tp30) REVERT: D 47 ASP cc_start: 0.9156 (p0) cc_final: 0.8767 (p0) REVERT: D 185 TYR cc_start: 0.9027 (t80) cc_final: 0.8677 (t80) REVERT: D 213 MET cc_start: 0.8437 (mmm) cc_final: 0.7134 (mmm) REVERT: E 3 ASP cc_start: 0.7933 (t0) cc_final: 0.7444 (t70) REVERT: E 47 ASP cc_start: 0.8919 (p0) cc_final: 0.8542 (p0) REVERT: E 185 TYR cc_start: 0.9033 (t80) cc_final: 0.8546 (t80) REVERT: F 3 ASP cc_start: 0.7997 (t0) cc_final: 0.7537 (t70) REVERT: F 55 ASN cc_start: 0.9145 (t0) cc_final: 0.8797 (t0) REVERT: G 3 ASP cc_start: 0.7458 (t0) cc_final: 0.7063 (t70) REVERT: G 47 ASP cc_start: 0.9129 (p0) cc_final: 0.8893 (p0) REVERT: G 53 ARG cc_start: 0.8290 (mtt90) cc_final: 0.8046 (mtt90) REVERT: G 55 ASN cc_start: 0.9159 (t0) cc_final: 0.8915 (t0) REVERT: H 3 ASP cc_start: 0.7598 (t0) cc_final: 0.7286 (t70) REVERT: H 47 ASP cc_start: 0.9167 (p0) cc_final: 0.8830 (p0) REVERT: H 55 ASN cc_start: 0.9288 (t0) cc_final: 0.8934 (t0) REVERT: H 82 ILE cc_start: 0.8755 (tt) cc_final: 0.8515 (tp) REVERT: H 98 TYR cc_start: 0.8748 (m-80) cc_final: 0.8450 (m-80) REVERT: I 3 ASP cc_start: 0.7672 (t0) cc_final: 0.7070 (t70) REVERT: I 98 TYR cc_start: 0.8740 (m-80) cc_final: 0.8478 (m-10) REVERT: I 206 LYS cc_start: 0.9088 (mttt) cc_final: 0.8452 (mttp) REVERT: J 3 ASP cc_start: 0.7983 (t0) cc_final: 0.7597 (t70) REVERT: J 55 ASN cc_start: 0.9155 (t0) cc_final: 0.8824 (t0) REVERT: K 3 ASP cc_start: 0.7936 (t0) cc_final: 0.7514 (t70) REVERT: K 47 ASP cc_start: 0.9072 (p0) cc_final: 0.8716 (p0) REVERT: K 82 ILE cc_start: 0.8806 (tt) cc_final: 0.8590 (tp) REVERT: K 104 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8410 (mt-10) REVERT: K 185 TYR cc_start: 0.9049 (t80) cc_final: 0.8577 (t80) REVERT: K 213 MET cc_start: 0.8397 (mmm) cc_final: 0.7037 (mmm) REVERT: L 3 ASP cc_start: 0.7685 (t0) cc_final: 0.7173 (t70) REVERT: L 55 ASN cc_start: 0.9257 (t0) cc_final: 0.8844 (t0) REVERT: L 206 LYS cc_start: 0.9150 (mttt) cc_final: 0.8474 (mttp) REVERT: L 224 ASN cc_start: 0.9087 (m-40) cc_final: 0.8876 (m110) outliers start: 84 outliers final: 43 residues processed: 609 average time/residue: 0.3564 time to fit residues: 323.5848 Evaluate side-chains 519 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 476 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 58 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 58 GLN B 81 GLN C 49 GLN C 58 GLN C 81 GLN D 49 GLN D 58 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 58 GLN F 49 GLN F 58 GLN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 58 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN H 58 GLN ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN I 81 GLN J 49 GLN J 58 GLN J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN K 58 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN L 58 GLN L 81 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21204 Z= 0.154 Angle : 0.546 8.789 28056 Z= 0.271 Chirality : 0.036 0.165 3024 Planarity : 0.004 0.036 3204 Dihedral : 10.213 58.158 3903 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.24 % Allowed : 16.48 % Favored : 80.29 % 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: -2.32 (0.15), residues: 2304 helix: -1.05 (0.11), residues: 1452 sheet: 0.92 (0.44), residues: 132 loop : -2.85 (0.18), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 45 HIS 0.002 0.001 HIS G 194 PHE 0.017 0.001 PHE H 30 TYR 0.020 0.001 TYR D 230 ARG 0.006 0.000 ARG F 53 *********************** 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 621 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 553 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7779 (t0) cc_final: 0.7430 (t70) REVERT: A 47 ASP cc_start: 0.9132 (p0) cc_final: 0.8769 (p0) REVERT: A 55 ASN cc_start: 0.9112 (t0) cc_final: 0.8630 (t0) REVERT: B 3 ASP cc_start: 0.7594 (t0) cc_final: 0.7056 (t70) REVERT: B 55 ASN cc_start: 0.9094 (t0) cc_final: 0.8709 (t0) REVERT: B 213 MET cc_start: 0.8293 (mmm) cc_final: 0.6856 (mmm) REVERT: C 55 ASN cc_start: 0.8996 (t0) cc_final: 0.8599 (t0) REVERT: D 3 ASP cc_start: 0.7830 (t0) cc_final: 0.7406 (t70) REVERT: D 47 ASP cc_start: 0.9087 (p0) cc_final: 0.8735 (p0) REVERT: E 3 ASP cc_start: 0.7887 (t0) cc_final: 0.7590 (t70) REVERT: E 55 ASN cc_start: 0.9175 (t0) cc_final: 0.8922 (t0) REVERT: E 162 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7575 (mtpp) REVERT: E 213 MET cc_start: 0.8295 (mmm) cc_final: 0.7096 (mmm) REVERT: F 3 ASP cc_start: 0.7900 (t0) cc_final: 0.7484 (t70) REVERT: F 55 ASN cc_start: 0.9076 (t0) cc_final: 0.8754 (t0) REVERT: F 213 MET cc_start: 0.8477 (mmm) cc_final: 0.7286 (mmm) REVERT: G 3 ASP cc_start: 0.7406 (t0) cc_final: 0.6900 (t70) REVERT: G 47 ASP cc_start: 0.9104 (p0) cc_final: 0.8873 (p0) REVERT: G 55 ASN cc_start: 0.9098 (t0) cc_final: 0.8788 (t0) REVERT: H 3 ASP cc_start: 0.7531 (t0) cc_final: 0.6958 (t70) REVERT: H 47 ASP cc_start: 0.9116 (p0) cc_final: 0.8766 (p0) REVERT: H 55 ASN cc_start: 0.9135 (t0) cc_final: 0.8808 (t0) REVERT: I 3 ASP cc_start: 0.7695 (t0) cc_final: 0.7274 (t70) REVERT: I 55 ASN cc_start: 0.9093 (t0) cc_final: 0.8720 (t0) REVERT: J 3 ASP cc_start: 0.7911 (t0) cc_final: 0.7538 (t70) REVERT: J 55 ASN cc_start: 0.9104 (t0) cc_final: 0.8747 (t0) REVERT: J 213 MET cc_start: 0.8482 (mmm) cc_final: 0.7325 (mmm) REVERT: K 3 ASP cc_start: 0.7861 (t0) cc_final: 0.7357 (t70) REVERT: K 47 ASP cc_start: 0.9015 (p0) cc_final: 0.8690 (p0) REVERT: K 55 ASN cc_start: 0.9144 (t0) cc_final: 0.8695 (t0) REVERT: L 3 ASP cc_start: 0.7665 (t0) cc_final: 0.7070 (t70) REVERT: L 55 ASN cc_start: 0.9095 (t0) cc_final: 0.8718 (t0) outliers start: 68 outliers final: 48 residues processed: 580 average time/residue: 0.3332 time to fit residues: 291.8236 Evaluate side-chains 538 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 490 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 0.0670 chunk 184 optimal weight: 4.9990 chunk 205 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 81 GLN D 63 ASN D 81 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN I 81 GLN J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21204 Z= 0.131 Angle : 0.524 9.263 28056 Z= 0.254 Chirality : 0.036 0.173 3024 Planarity : 0.003 0.031 3204 Dihedral : 9.054 58.055 3876 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.90 % Allowed : 19.90 % Favored : 77.19 % 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: -0.77 (0.16), residues: 2304 helix: 0.42 (0.13), residues: 1452 sheet: 0.54 (0.42), residues: 132 loop : -2.65 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 45 HIS 0.009 0.000 HIS C 95 PHE 0.016 0.001 PHE I 30 TYR 0.016 0.001 TYR I 92 ARG 0.006 0.000 ARG H 53 *********************** 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 586 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 525 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7579 (t0) cc_final: 0.7233 (t70) REVERT: A 47 ASP cc_start: 0.9158 (p0) cc_final: 0.8620 (p0) REVERT: A 55 ASN cc_start: 0.9072 (t0) cc_final: 0.8839 (t0) REVERT: B 3 ASP cc_start: 0.7467 (t0) cc_final: 0.6943 (t70) REVERT: B 55 ASN cc_start: 0.9025 (t0) cc_final: 0.8669 (t0) REVERT: C 3 ASP cc_start: 0.7596 (t0) cc_final: 0.6860 (t70) REVERT: C 55 ASN cc_start: 0.8957 (t0) cc_final: 0.8604 (t0) REVERT: D 3 ASP cc_start: 0.7714 (t0) cc_final: 0.7216 (t70) REVERT: D 47 ASP cc_start: 0.9094 (p0) cc_final: 0.8574 (p0) REVERT: D 55 ASN cc_start: 0.9109 (t0) cc_final: 0.8851 (t0) REVERT: E 3 ASP cc_start: 0.7799 (t0) cc_final: 0.7480 (t70) REVERT: E 47 ASP cc_start: 0.8780 (p0) cc_final: 0.8340 (p0) REVERT: E 55 ASN cc_start: 0.9112 (t0) cc_final: 0.8831 (t0) REVERT: E 162 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7465 (mtpp) REVERT: E 213 MET cc_start: 0.8301 (mmm) cc_final: 0.6956 (mmm) REVERT: F 3 ASP cc_start: 0.7768 (t0) cc_final: 0.7318 (t70) REVERT: F 55 ASN cc_start: 0.9045 (t0) cc_final: 0.8772 (t0) REVERT: F 213 MET cc_start: 0.8513 (mmm) cc_final: 0.7241 (mmm) REVERT: G 3 ASP cc_start: 0.7303 (t0) cc_final: 0.6817 (t70) REVERT: G 42 GLU cc_start: 0.7407 (tp30) cc_final: 0.7195 (tp30) REVERT: G 47 ASP cc_start: 0.9124 (p0) cc_final: 0.8721 (p0) REVERT: G 55 ASN cc_start: 0.9034 (t0) cc_final: 0.8767 (t0) REVERT: H 3 ASP cc_start: 0.7408 (t0) cc_final: 0.6829 (t70) REVERT: H 42 GLU cc_start: 0.7454 (tp30) cc_final: 0.7177 (tp30) REVERT: H 47 ASP cc_start: 0.9175 (p0) cc_final: 0.8806 (p0) REVERT: H 55 ASN cc_start: 0.9077 (t0) cc_final: 0.8787 (t0) REVERT: I 3 ASP cc_start: 0.7644 (t0) cc_final: 0.7203 (t70) REVERT: I 55 ASN cc_start: 0.9039 (t0) cc_final: 0.8658 (t0) REVERT: I 162 LYS cc_start: 0.7621 (mtpt) cc_final: 0.7401 (mtpp) REVERT: J 3 ASP cc_start: 0.7732 (t0) cc_final: 0.7351 (t70) REVERT: J 55 ASN cc_start: 0.9038 (t0) cc_final: 0.8758 (t0) REVERT: J 213 MET cc_start: 0.8518 (mmm) cc_final: 0.7285 (mmm) REVERT: K 3 ASP cc_start: 0.7756 (t0) cc_final: 0.7428 (t70) REVERT: K 47 ASP cc_start: 0.9037 (p0) cc_final: 0.8537 (p0) REVERT: K 55 ASN cc_start: 0.9099 (t0) cc_final: 0.8878 (t0) REVERT: L 3 ASP cc_start: 0.7587 (t0) cc_final: 0.7008 (t70) REVERT: L 55 ASN cc_start: 0.9064 (t0) cc_final: 0.8741 (t0) outliers start: 61 outliers final: 46 residues processed: 545 average time/residue: 0.3285 time to fit residues: 274.5723 Evaluate side-chains 543 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 497 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 187 CYS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN J 63 ASN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21204 Z= 0.269 Angle : 0.581 8.962 28056 Z= 0.289 Chirality : 0.039 0.138 3024 Planarity : 0.004 0.038 3204 Dihedral : 9.647 58.512 3863 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.19 % Allowed : 21.71 % Favored : 74.10 % 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 (0.18), residues: 2304 helix: 1.22 (0.14), residues: 1440 sheet: 0.72 (0.43), residues: 132 loop : -2.19 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 25 HIS 0.007 0.001 HIS C 95 PHE 0.015 0.001 PHE I 161 TYR 0.023 0.001 TYR I 155 ARG 0.005 0.000 ARG F 53 *********************** 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 602 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 514 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7599 (t0) cc_final: 0.7258 (t70) REVERT: A 47 ASP cc_start: 0.9174 (p0) cc_final: 0.8596 (p0) REVERT: A 55 ASN cc_start: 0.9189 (t0) cc_final: 0.8750 (t0) REVERT: A 213 MET cc_start: 0.8480 (mmm) cc_final: 0.7686 (mmm) REVERT: B 3 ASP cc_start: 0.7495 (t0) cc_final: 0.7038 (t70) REVERT: B 47 ASP cc_start: 0.9141 (p0) cc_final: 0.8622 (p0) REVERT: B 55 ASN cc_start: 0.9153 (t0) cc_final: 0.8822 (t0) REVERT: C 3 ASP cc_start: 0.7677 (t0) cc_final: 0.7022 (t70) REVERT: C 47 ASP cc_start: 0.9113 (p0) cc_final: 0.8686 (p0) REVERT: C 55 ASN cc_start: 0.9108 (t0) cc_final: 0.8816 (t0) REVERT: D 3 ASP cc_start: 0.7710 (t0) cc_final: 0.7403 (t70) REVERT: D 47 ASP cc_start: 0.9135 (p0) cc_final: 0.8583 (p0) REVERT: D 55 ASN cc_start: 0.9192 (t0) cc_final: 0.8737 (t0) REVERT: D 213 MET cc_start: 0.8476 (mmm) cc_final: 0.7714 (mmm) REVERT: E 3 ASP cc_start: 0.7775 (t0) cc_final: 0.7195 (t70) REVERT: E 47 ASP cc_start: 0.8929 (p0) cc_final: 0.8503 (p0) REVERT: E 55 ASN cc_start: 0.9168 (t0) cc_final: 0.8848 (t0) REVERT: E 213 MET cc_start: 0.8380 (mmm) cc_final: 0.7175 (mmm) REVERT: F 3 ASP cc_start: 0.7623 (t0) cc_final: 0.7226 (t70) REVERT: F 47 ASP cc_start: 0.9078 (p0) cc_final: 0.8675 (p0) REVERT: F 55 ASN cc_start: 0.9145 (t0) cc_final: 0.8893 (t0) REVERT: G 3 ASP cc_start: 0.7391 (t0) cc_final: 0.6989 (t70) REVERT: G 47 ASP cc_start: 0.9154 (p0) cc_final: 0.8679 (p0) REVERT: G 55 ASN cc_start: 0.9132 (t0) cc_final: 0.8883 (t0) REVERT: H 3 ASP cc_start: 0.7466 (t0) cc_final: 0.6923 (t70) REVERT: H 42 GLU cc_start: 0.7622 (tp30) cc_final: 0.7321 (tp30) REVERT: H 47 ASP cc_start: 0.9197 (p0) cc_final: 0.8632 (p0) REVERT: H 55 ASN cc_start: 0.9173 (t0) cc_final: 0.8686 (t0) REVERT: I 3 ASP cc_start: 0.7727 (t0) cc_final: 0.7067 (t70) REVERT: I 47 ASP cc_start: 0.8859 (p0) cc_final: 0.8345 (p0) REVERT: I 55 ASN cc_start: 0.9142 (t0) cc_final: 0.8805 (t0) REVERT: I 213 MET cc_start: 0.8392 (mmm) cc_final: 0.7137 (mmm) REVERT: J 3 ASP cc_start: 0.7640 (t0) cc_final: 0.7224 (t70) REVERT: J 47 ASP cc_start: 0.9101 (p0) cc_final: 0.8707 (p0) REVERT: J 55 ASN cc_start: 0.9153 (t0) cc_final: 0.8896 (t0) REVERT: K 3 ASP cc_start: 0.7690 (t0) cc_final: 0.7387 (t70) REVERT: K 47 ASP cc_start: 0.9098 (p0) cc_final: 0.8573 (p0) REVERT: K 55 ASN cc_start: 0.9188 (t0) cc_final: 0.8729 (t0) REVERT: K 166 GLU cc_start: 0.8648 (tp30) cc_final: 0.8442 (tp30) REVERT: L 3 ASP cc_start: 0.7664 (t0) cc_final: 0.7193 (t70) REVERT: L 47 ASP cc_start: 0.9140 (p0) cc_final: 0.8606 (p0) REVERT: L 55 ASN cc_start: 0.9158 (t0) cc_final: 0.8858 (t0) REVERT: L 213 MET cc_start: 0.8387 (mmm) cc_final: 0.7323 (mmm) outliers start: 88 outliers final: 59 residues processed: 551 average time/residue: 0.3241 time to fit residues: 276.6026 Evaluate side-chains 556 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 497 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 224 ASN Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 187 CYS Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 89 THR 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: 9.9990 chunk 3 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 81 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21204 Z= 0.150 Angle : 0.516 9.916 28056 Z= 0.251 Chirality : 0.037 0.125 3024 Planarity : 0.003 0.035 3204 Dihedral : 8.818 59.986 3863 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.05 % Allowed : 23.71 % Favored : 73.24 % 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: 0.73 (0.17), residues: 2304 helix: 1.59 (0.13), residues: 1464 sheet: 0.53 (0.42), residues: 132 loop : -1.97 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 45 HIS 0.006 0.000 HIS C 95 PHE 0.012 0.001 PHE H 30 TYR 0.017 0.001 TYR G 230 ARG 0.003 0.000 ARG H 53 *********************** 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 606 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 542 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7465 (t0) cc_final: 0.6895 (t70) REVERT: A 47 ASP cc_start: 0.9116 (p0) cc_final: 0.8244 (p0) REVERT: A 55 ASN cc_start: 0.9106 (t0) cc_final: 0.8882 (t0) REVERT: A 213 MET cc_start: 0.8462 (mmm) cc_final: 0.7398 (mmm) REVERT: B 3 ASP cc_start: 0.7422 (t0) cc_final: 0.6707 (t70) REVERT: B 47 ASP cc_start: 0.9113 (p0) cc_final: 0.8504 (p0) REVERT: B 55 ASN cc_start: 0.9068 (t0) cc_final: 0.8766 (t0) REVERT: C 3 ASP cc_start: 0.7563 (t0) cc_final: 0.6848 (t70) REVERT: C 47 ASP cc_start: 0.9059 (p0) cc_final: 0.8125 (p0) REVERT: C 55 ASN cc_start: 0.9027 (t0) cc_final: 0.8722 (t0) REVERT: C 152 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8750 (mt) REVERT: D 3 ASP cc_start: 0.7566 (t0) cc_final: 0.7253 (t70) REVERT: D 47 ASP cc_start: 0.9076 (p0) cc_final: 0.8261 (p0) REVERT: D 55 ASN cc_start: 0.9109 (t0) cc_final: 0.8889 (t0) REVERT: D 213 MET cc_start: 0.8446 (mmm) cc_final: 0.7387 (mmm) REVERT: E 3 ASP cc_start: 0.7665 (t0) cc_final: 0.7264 (t70) REVERT: E 47 ASP cc_start: 0.8909 (p0) cc_final: 0.8430 (p0) REVERT: E 55 ASN cc_start: 0.9079 (t0) cc_final: 0.8785 (t0) REVERT: F 3 ASP cc_start: 0.7489 (t0) cc_final: 0.6796 (t70) REVERT: F 47 ASP cc_start: 0.9048 (p0) cc_final: 0.8614 (p0) REVERT: F 55 ASN cc_start: 0.9072 (t0) cc_final: 0.8824 (t0) REVERT: F 161 PHE cc_start: 0.8772 (m-80) cc_final: 0.8482 (m-80) REVERT: F 213 MET cc_start: 0.8348 (mmm) cc_final: 0.7501 (mmm) REVERT: G 3 ASP cc_start: 0.7347 (t0) cc_final: 0.6832 (t70) REVERT: G 47 ASP cc_start: 0.9062 (p0) cc_final: 0.8153 (p0) REVERT: G 55 ASN cc_start: 0.9051 (t0) cc_final: 0.8798 (t0) REVERT: G 152 LEU cc_start: 0.9393 (tp) cc_final: 0.9002 (mt) REVERT: G 213 MET cc_start: 0.8311 (mmm) cc_final: 0.7512 (mmm) REVERT: H 3 ASP cc_start: 0.7438 (t0) cc_final: 0.6824 (t70) REVERT: H 42 GLU cc_start: 0.7612 (tp30) cc_final: 0.7330 (tp30) REVERT: H 47 ASP cc_start: 0.9119 (p0) cc_final: 0.8206 (p0) REVERT: H 55 ASN cc_start: 0.9082 (t0) cc_final: 0.8830 (t0) REVERT: I 3 ASP cc_start: 0.7613 (t0) cc_final: 0.6873 (t70) REVERT: I 47 ASP cc_start: 0.8799 (p0) cc_final: 0.7903 (p0) REVERT: I 55 ASN cc_start: 0.9069 (t0) cc_final: 0.8729 (t0) REVERT: I 152 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8725 (mt) REVERT: I 162 LYS cc_start: 0.7510 (mtpt) cc_final: 0.7252 (mtpp) REVERT: J 3 ASP cc_start: 0.7485 (t0) cc_final: 0.6820 (t70) REVERT: J 47 ASP cc_start: 0.9074 (p0) cc_final: 0.8621 (p0) REVERT: J 55 ASN cc_start: 0.9064 (t0) cc_final: 0.8793 (t0) REVERT: J 213 MET cc_start: 0.8317 (mmm) cc_final: 0.7426 (mmm) REVERT: K 3 ASP cc_start: 0.7532 (t0) cc_final: 0.6994 (t70) REVERT: K 47 ASP cc_start: 0.9041 (p0) cc_final: 0.8247 (p0) REVERT: K 55 ASN cc_start: 0.9103 (t0) cc_final: 0.8865 (t0) REVERT: K 166 GLU cc_start: 0.8617 (tp30) cc_final: 0.8411 (tp30) REVERT: K 213 MET cc_start: 0.8409 (mmm) cc_final: 0.7294 (mmm) REVERT: L 3 ASP cc_start: 0.7578 (t0) cc_final: 0.6852 (t70) REVERT: L 47 ASP cc_start: 0.9111 (p0) cc_final: 0.8521 (p0) REVERT: L 55 ASN cc_start: 0.9083 (t0) cc_final: 0.8790 (t0) outliers start: 64 outliers final: 43 residues processed: 560 average time/residue: 0.3214 time to fit residues: 276.7888 Evaluate side-chains 555 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 510 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 187 CYS Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21204 Z= 0.134 Angle : 0.520 10.668 28056 Z= 0.251 Chirality : 0.037 0.155 3024 Planarity : 0.003 0.035 3204 Dihedral : 8.502 59.969 3852 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.81 % Allowed : 23.86 % Favored : 73.33 % 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: 1.00 (0.17), residues: 2304 helix: 1.81 (0.13), residues: 1464 sheet: 0.62 (0.43), residues: 132 loop : -1.88 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 45 HIS 0.005 0.000 HIS C 95 PHE 0.011 0.001 PHE I 30 TYR 0.027 0.001 TYR E 155 ARG 0.003 0.000 ARG H 53 *********************** 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 610 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 551 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7427 (t0) cc_final: 0.6855 (t70) REVERT: A 47 ASP cc_start: 0.9082 (p0) cc_final: 0.8271 (p0) REVERT: A 55 ASN cc_start: 0.9066 (t0) cc_final: 0.8853 (t0) REVERT: B 3 ASP cc_start: 0.7398 (t0) cc_final: 0.6682 (t70) REVERT: B 47 ASP cc_start: 0.9066 (p0) cc_final: 0.8196 (p0) REVERT: B 55 ASN cc_start: 0.9027 (t0) cc_final: 0.8690 (t0) REVERT: C 3 ASP cc_start: 0.7527 (t0) cc_final: 0.6828 (t70) REVERT: C 47 ASP cc_start: 0.9018 (p0) cc_final: 0.8197 (p0) REVERT: C 55 ASN cc_start: 0.8991 (t0) cc_final: 0.8699 (t0) REVERT: C 152 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8766 (mt) REVERT: D 3 ASP cc_start: 0.7517 (t0) cc_final: 0.7174 (t70) REVERT: D 47 ASP cc_start: 0.9041 (p0) cc_final: 0.8293 (p0) REVERT: D 55 ASN cc_start: 0.9056 (t0) cc_final: 0.8844 (t0) REVERT: E 3 ASP cc_start: 0.7627 (t0) cc_final: 0.7246 (t70) REVERT: E 42 GLU cc_start: 0.7910 (tp30) cc_final: 0.7651 (tp30) REVERT: E 47 ASP cc_start: 0.8885 (p0) cc_final: 0.8352 (p0) REVERT: E 55 ASN cc_start: 0.9026 (t0) cc_final: 0.8680 (t0) REVERT: E 161 PHE cc_start: 0.8603 (m-80) cc_final: 0.8368 (m-80) REVERT: E 162 LYS cc_start: 0.7469 (mtpt) cc_final: 0.7186 (mtpp) REVERT: F 3 ASP cc_start: 0.7451 (t0) cc_final: 0.6786 (t70) REVERT: F 47 ASP cc_start: 0.9007 (p0) cc_final: 0.8168 (p0) REVERT: F 55 ASN cc_start: 0.9044 (t0) cc_final: 0.8807 (t0) REVERT: G 3 ASP cc_start: 0.7347 (t0) cc_final: 0.6819 (t70) REVERT: G 47 ASP cc_start: 0.9009 (p0) cc_final: 0.8192 (p0) REVERT: G 55 ASN cc_start: 0.9011 (t0) cc_final: 0.8769 (t0) REVERT: G 152 LEU cc_start: 0.9371 (tp) cc_final: 0.9015 (mt) REVERT: G 213 MET cc_start: 0.8349 (mmm) cc_final: 0.7464 (mmm) REVERT: H 3 ASP cc_start: 0.7441 (t0) cc_final: 0.6815 (t70) REVERT: H 42 GLU cc_start: 0.7591 (tp30) cc_final: 0.7338 (tp30) REVERT: H 47 ASP cc_start: 0.9074 (p0) cc_final: 0.8233 (p0) REVERT: H 55 ASN cc_start: 0.9033 (t0) cc_final: 0.8793 (t0) REVERT: I 3 ASP cc_start: 0.7601 (t0) cc_final: 0.6851 (t70) REVERT: I 47 ASP cc_start: 0.8782 (p0) cc_final: 0.7930 (p0) REVERT: I 55 ASN cc_start: 0.9033 (t0) cc_final: 0.8687 (t0) REVERT: I 152 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8728 (mt) REVERT: I 162 LYS cc_start: 0.7466 (mtpt) cc_final: 0.7194 (mtpp) REVERT: J 3 ASP cc_start: 0.7435 (t0) cc_final: 0.6760 (t70) REVERT: J 47 ASP cc_start: 0.9033 (p0) cc_final: 0.8215 (p0) REVERT: J 55 ASN cc_start: 0.9038 (t0) cc_final: 0.8780 (t0) REVERT: K 3 ASP cc_start: 0.7509 (t0) cc_final: 0.7216 (t70) REVERT: K 47 ASP cc_start: 0.9012 (p0) cc_final: 0.8296 (p0) REVERT: K 55 ASN cc_start: 0.9041 (t0) cc_final: 0.8811 (t0) REVERT: K 166 GLU cc_start: 0.8588 (tp30) cc_final: 0.8375 (tp30) REVERT: K 213 MET cc_start: 0.8349 (mmm) cc_final: 0.7142 (mmm) REVERT: L 3 ASP cc_start: 0.7566 (t0) cc_final: 0.6861 (t70) REVERT: L 47 ASP cc_start: 0.9080 (p0) cc_final: 0.8213 (p0) REVERT: L 55 ASN cc_start: 0.9038 (t0) cc_final: 0.8700 (t0) REVERT: L 213 MET cc_start: 0.8431 (mmm) cc_final: 0.7467 (mmm) outliers start: 59 outliers final: 45 residues processed: 567 average time/residue: 0.3126 time to fit residues: 273.6849 Evaluate side-chains 568 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 521 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 187 CYS Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21204 Z= 0.223 Angle : 0.562 10.078 28056 Z= 0.275 Chirality : 0.039 0.187 3024 Planarity : 0.003 0.037 3204 Dihedral : 8.917 59.738 3852 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.29 % Allowed : 24.52 % Favored : 72.19 % 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: 1.09 (0.18), residues: 2304 helix: 1.87 (0.13), residues: 1464 sheet: 0.55 (0.42), residues: 132 loop : -1.78 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 174 HIS 0.002 0.001 HIS C 95 PHE 0.014 0.001 PHE H 161 TYR 0.021 0.001 TYR H 155 ARG 0.003 0.000 ARG A 53 *********************** 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 588 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 519 time to evaluate : 2.299 Fit side-chains revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7502 (t0) cc_final: 0.6922 (t70) REVERT: A 47 ASP cc_start: 0.9107 (p0) cc_final: 0.8237 (p0) REVERT: A 55 ASN cc_start: 0.9134 (t0) cc_final: 0.8711 (t0) REVERT: A 161 PHE cc_start: 0.8693 (m-80) cc_final: 0.8431 (m-80) REVERT: A 213 MET cc_start: 0.8431 (mmm) cc_final: 0.7427 (mmm) REVERT: B 3 ASP cc_start: 0.7500 (t0) cc_final: 0.6795 (t70) REVERT: B 47 ASP cc_start: 0.9098 (p0) cc_final: 0.8209 (p0) REVERT: B 55 ASN cc_start: 0.9123 (t0) cc_final: 0.8818 (t0) REVERT: B 213 MET cc_start: 0.8327 (mmm) cc_final: 0.7543 (mmm) REVERT: C 3 ASP cc_start: 0.7583 (t0) cc_final: 0.6892 (t70) REVERT: C 47 ASP cc_start: 0.9044 (p0) cc_final: 0.8193 (p0) REVERT: C 55 ASN cc_start: 0.9077 (t0) cc_final: 0.8809 (t0) REVERT: C 152 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8761 (mt) REVERT: C 213 MET cc_start: 0.8377 (mmm) cc_final: 0.7398 (mmm) REVERT: D 3 ASP cc_start: 0.7556 (t0) cc_final: 0.7228 (t70) REVERT: D 47 ASP cc_start: 0.9064 (p0) cc_final: 0.8259 (p0) REVERT: D 55 ASN cc_start: 0.9131 (t0) cc_final: 0.8691 (t0) REVERT: D 161 PHE cc_start: 0.8701 (m-80) cc_final: 0.8422 (m-80) REVERT: D 213 MET cc_start: 0.8417 (mmm) cc_final: 0.7411 (mmm) REVERT: E 3 ASP cc_start: 0.7711 (t0) cc_final: 0.7312 (t70) REVERT: E 47 ASP cc_start: 0.8942 (p0) cc_final: 0.8413 (p0) REVERT: E 55 ASN cc_start: 0.9123 (t0) cc_final: 0.8814 (t0) REVERT: E 162 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7308 (mtpp) REVERT: F 3 ASP cc_start: 0.7490 (t0) cc_final: 0.6835 (t70) REVERT: F 47 ASP cc_start: 0.9048 (p0) cc_final: 0.8152 (p0) REVERT: F 55 ASN cc_start: 0.9112 (t0) cc_final: 0.8897 (t0) REVERT: F 213 MET cc_start: 0.8457 (mmm) cc_final: 0.7518 (mmm) REVERT: G 3 ASP cc_start: 0.7471 (t0) cc_final: 0.6956 (t70) REVERT: G 47 ASP cc_start: 0.9052 (p0) cc_final: 0.8174 (p0) REVERT: G 55 ASN cc_start: 0.9095 (t0) cc_final: 0.8871 (t0) REVERT: G 103 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8957 (mt-10) REVERT: G 152 LEU cc_start: 0.9408 (tp) cc_final: 0.9049 (mt) REVERT: H 3 ASP cc_start: 0.7517 (t0) cc_final: 0.6895 (t70) REVERT: H 42 GLU cc_start: 0.7621 (tp30) cc_final: 0.7335 (tp30) REVERT: H 47 ASP cc_start: 0.9093 (p0) cc_final: 0.8215 (p0) REVERT: H 55 ASN cc_start: 0.9140 (t0) cc_final: 0.8675 (t0) REVERT: H 161 PHE cc_start: 0.8669 (m-80) cc_final: 0.8428 (m-80) REVERT: I 3 ASP cc_start: 0.7653 (t0) cc_final: 0.6942 (t70) REVERT: I 47 ASP cc_start: 0.8843 (p0) cc_final: 0.7977 (p0) REVERT: I 55 ASN cc_start: 0.9122 (t0) cc_final: 0.8818 (t0) REVERT: I 152 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8738 (mt) REVERT: I 161 PHE cc_start: 0.8708 (m-80) cc_final: 0.8493 (m-80) REVERT: I 162 LYS cc_start: 0.7581 (mtpt) cc_final: 0.7330 (mtpp) REVERT: J 3 ASP cc_start: 0.7504 (t0) cc_final: 0.6836 (t70) REVERT: J 47 ASP cc_start: 0.9074 (p0) cc_final: 0.8203 (p0) REVERT: J 55 ASN cc_start: 0.9113 (t0) cc_final: 0.8872 (t0) REVERT: K 3 ASP cc_start: 0.7548 (t0) cc_final: 0.7237 (t70) REVERT: K 47 ASP cc_start: 0.9046 (p0) cc_final: 0.8267 (p0) REVERT: K 55 ASN cc_start: 0.9136 (t0) cc_final: 0.8675 (t0) REVERT: K 166 GLU cc_start: 0.8619 (tp30) cc_final: 0.8410 (tp30) REVERT: K 213 MET cc_start: 0.8339 (mmm) cc_final: 0.7142 (mmm) REVERT: L 3 ASP cc_start: 0.7645 (t0) cc_final: 0.6989 (t70) REVERT: L 47 ASP cc_start: 0.9097 (p0) cc_final: 0.8225 (p0) REVERT: L 55 ASN cc_start: 0.9129 (t0) cc_final: 0.8822 (t0) REVERT: L 213 MET cc_start: 0.8364 (mmm) cc_final: 0.7231 (mmm) outliers start: 69 outliers final: 47 residues processed: 537 average time/residue: 0.3240 time to fit residues: 268.7043 Evaluate side-chains 553 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 504 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 187 CYS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 172 optimal weight: 0.0980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21204 Z= 0.133 Angle : 0.528 11.092 28056 Z= 0.256 Chirality : 0.037 0.175 3024 Planarity : 0.003 0.036 3204 Dihedral : 8.243 59.018 3852 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.76 % Allowed : 25.19 % Favored : 72.05 % 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: 1.02 (0.17), residues: 2304 helix: 1.90 (0.13), residues: 1476 sheet: 0.70 (0.43), residues: 132 loop : -2.14 (0.19), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 45 HIS 0.002 0.000 HIS J 95 PHE 0.010 0.001 PHE J 161 TYR 0.020 0.001 TYR A 230 ARG 0.002 0.000 ARG H 53 *********************** 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 612 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 554 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7406 (t0) cc_final: 0.6802 (t70) REVERT: A 47 ASP cc_start: 0.9059 (p0) cc_final: 0.8310 (p0) REVERT: A 55 ASN cc_start: 0.9064 (t0) cc_final: 0.8855 (t0) REVERT: A 213 MET cc_start: 0.8413 (mmm) cc_final: 0.7274 (mmm) REVERT: B 3 ASP cc_start: 0.7425 (t0) cc_final: 0.6708 (t70) REVERT: B 47 ASP cc_start: 0.9038 (p0) cc_final: 0.8243 (p0) REVERT: B 55 ASN cc_start: 0.9021 (t0) cc_final: 0.8710 (t0) REVERT: B 162 LYS cc_start: 0.7340 (mtpt) cc_final: 0.7042 (mtpp) REVERT: B 213 MET cc_start: 0.8306 (mmm) cc_final: 0.7370 (mmm) REVERT: C 3 ASP cc_start: 0.7510 (t0) cc_final: 0.6896 (t70) REVERT: C 47 ASP cc_start: 0.8977 (p0) cc_final: 0.8251 (p0) REVERT: C 55 ASN cc_start: 0.8997 (t0) cc_final: 0.8719 (t0) REVERT: C 152 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8741 (mt) REVERT: C 213 MET cc_start: 0.8372 (mmm) cc_final: 0.7287 (mmm) REVERT: D 3 ASP cc_start: 0.7454 (t0) cc_final: 0.6821 (t70) REVERT: D 47 ASP cc_start: 0.9000 (p0) cc_final: 0.8312 (p0) REVERT: D 55 ASN cc_start: 0.9041 (t0) cc_final: 0.8829 (t0) REVERT: D 213 MET cc_start: 0.8392 (mmm) cc_final: 0.7235 (mmm) REVERT: E 3 ASP cc_start: 0.7609 (t0) cc_final: 0.6933 (t70) REVERT: E 47 ASP cc_start: 0.8879 (p0) cc_final: 0.8143 (p0) REVERT: E 55 ASN cc_start: 0.9018 (t0) cc_final: 0.8699 (t0) REVERT: E 103 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8902 (mt-10) REVERT: E 162 LYS cc_start: 0.7481 (mtpt) cc_final: 0.7193 (mtpp) REVERT: F 3 ASP cc_start: 0.7444 (t0) cc_final: 0.6778 (t70) REVERT: F 47 ASP cc_start: 0.8978 (p0) cc_final: 0.8199 (p0) REVERT: F 55 ASN cc_start: 0.9055 (t0) cc_final: 0.8835 (t0) REVERT: F 213 MET cc_start: 0.8439 (mmm) cc_final: 0.7394 (mmm) REVERT: G 3 ASP cc_start: 0.7390 (t0) cc_final: 0.6868 (t70) REVERT: G 47 ASP cc_start: 0.8975 (p0) cc_final: 0.8201 (p0) REVERT: G 55 ASN cc_start: 0.9019 (t0) cc_final: 0.8778 (t0) REVERT: G 103 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8938 (mt-10) REVERT: G 152 LEU cc_start: 0.9357 (tp) cc_final: 0.9039 (mt) REVERT: G 161 PHE cc_start: 0.8643 (m-80) cc_final: 0.8437 (m-80) REVERT: G 162 LYS cc_start: 0.7402 (mtpt) cc_final: 0.7115 (mtpp) REVERT: H 3 ASP cc_start: 0.7462 (t0) cc_final: 0.6899 (t70) REVERT: H 47 ASP cc_start: 0.9024 (p0) cc_final: 0.8257 (p0) REVERT: H 55 ASN cc_start: 0.9042 (t0) cc_final: 0.8806 (t0) REVERT: I 3 ASP cc_start: 0.7568 (t0) cc_final: 0.6828 (t70) REVERT: I 47 ASP cc_start: 0.8785 (p0) cc_final: 0.7981 (p0) REVERT: I 55 ASN cc_start: 0.9036 (t0) cc_final: 0.8717 (t0) REVERT: I 152 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8724 (mt) REVERT: I 162 LYS cc_start: 0.7498 (mtpt) cc_final: 0.7215 (mtpp) REVERT: J 3 ASP cc_start: 0.7448 (t0) cc_final: 0.6736 (t70) REVERT: J 47 ASP cc_start: 0.8991 (p0) cc_final: 0.8252 (p0) REVERT: J 55 ASN cc_start: 0.9034 (t0) cc_final: 0.8777 (t0) REVERT: J 213 MET cc_start: 0.8242 (mmm) cc_final: 0.7317 (mmm) REVERT: K 3 ASP cc_start: 0.7460 (t0) cc_final: 0.6871 (t70) REVERT: K 47 ASP cc_start: 0.8995 (p0) cc_final: 0.8327 (p0) REVERT: K 55 ASN cc_start: 0.9038 (t0) cc_final: 0.8804 (t0) REVERT: K 161 PHE cc_start: 0.8649 (m-80) cc_final: 0.8418 (m-80) REVERT: K 166 GLU cc_start: 0.8586 (tp30) cc_final: 0.8384 (tp30) REVERT: L 3 ASP cc_start: 0.7584 (t0) cc_final: 0.6884 (t70) REVERT: L 47 ASP cc_start: 0.9050 (p0) cc_final: 0.8274 (p0) REVERT: L 55 ASN cc_start: 0.9042 (t0) cc_final: 0.8712 (t0) REVERT: L 162 LYS cc_start: 0.7305 (mtpt) cc_final: 0.7006 (mtpp) REVERT: L 213 MET cc_start: 0.8327 (mmm) cc_final: 0.7104 (mmm) outliers start: 58 outliers final: 44 residues processed: 570 average time/residue: 0.3241 time to fit residues: 283.2921 Evaluate side-chains 581 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 535 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 187 CYS Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 225 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21204 Z= 0.303 Angle : 0.620 10.762 28056 Z= 0.305 Chirality : 0.041 0.170 3024 Planarity : 0.004 0.038 3204 Dihedral : 9.250 59.733 3852 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.76 % Allowed : 25.52 % Favored : 71.71 % 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: 0.92 (0.17), residues: 2304 helix: 1.82 (0.13), residues: 1476 sheet: 0.56 (0.41), residues: 132 loop : -2.16 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 174 HIS 0.003 0.001 HIS C 95 PHE 0.031 0.001 PHE H 30 TYR 0.027 0.002 TYR G 155 ARG 0.004 0.000 ARG F 53 *********************** 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 561 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 503 time to evaluate : 2.317 Fit side-chains REVERT: A 3 ASP cc_start: 0.7551 (t0) cc_final: 0.6956 (t70) REVERT: A 47 ASP cc_start: 0.9146 (p0) cc_final: 0.8256 (p0) REVERT: A 161 PHE cc_start: 0.8739 (m-80) cc_final: 0.8501 (m-80) REVERT: A 213 MET cc_start: 0.8386 (mmm) cc_final: 0.7233 (mmm) REVERT: B 3 ASP cc_start: 0.7591 (t0) cc_final: 0.6875 (t70) REVERT: B 47 ASP cc_start: 0.9129 (p0) cc_final: 0.8511 (p0) REVERT: B 55 ASN cc_start: 0.9150 (t0) cc_final: 0.8881 (t0) REVERT: B 103 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8992 (mt-10) REVERT: B 213 MET cc_start: 0.8343 (mmm) cc_final: 0.7494 (mmm) REVERT: C 3 ASP cc_start: 0.7658 (t0) cc_final: 0.7000 (t70) REVERT: C 47 ASP cc_start: 0.9072 (p0) cc_final: 0.8190 (p0) REVERT: C 55 ASN cc_start: 0.9135 (t0) cc_final: 0.8884 (t0) REVERT: C 152 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8767 (mt) REVERT: D 3 ASP cc_start: 0.7584 (t0) cc_final: 0.7236 (t70) REVERT: D 47 ASP cc_start: 0.9109 (p0) cc_final: 0.8262 (p0) REVERT: D 55 ASN cc_start: 0.9188 (t0) cc_final: 0.8762 (t0) REVERT: D 161 PHE cc_start: 0.8744 (m-80) cc_final: 0.8493 (m-80) REVERT: D 213 MET cc_start: 0.8378 (mmm) cc_final: 0.7220 (mmm) REVERT: E 3 ASP cc_start: 0.7690 (t0) cc_final: 0.7028 (t70) REVERT: E 47 ASP cc_start: 0.8980 (p0) cc_final: 0.8479 (p0) REVERT: E 55 ASN cc_start: 0.9156 (t0) cc_final: 0.8878 (t0) REVERT: E 103 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8952 (mt-10) REVERT: F 3 ASP cc_start: 0.7544 (t0) cc_final: 0.6864 (t70) REVERT: F 47 ASP cc_start: 0.9083 (p0) cc_final: 0.8155 (p0) REVERT: F 213 MET cc_start: 0.8424 (mmm) cc_final: 0.7397 (mmm) REVERT: G 3 ASP cc_start: 0.7558 (t0) cc_final: 0.7026 (t70) REVERT: G 47 ASP cc_start: 0.9069 (p0) cc_final: 0.8145 (p0) REVERT: G 55 ASN cc_start: 0.9146 (t0) cc_final: 0.8935 (t0) REVERT: G 103 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8965 (mt-10) REVERT: G 152 LEU cc_start: 0.9470 (tp) cc_final: 0.9103 (mt) REVERT: H 3 ASP cc_start: 0.7566 (t0) cc_final: 0.6927 (t70) REVERT: H 47 ASP cc_start: 0.9126 (p0) cc_final: 0.8227 (p0) REVERT: H 55 ASN cc_start: 0.9189 (t0) cc_final: 0.8749 (t0) REVERT: H 161 PHE cc_start: 0.8696 (m-80) cc_final: 0.8481 (m-80) REVERT: I 3 ASP cc_start: 0.7692 (t0) cc_final: 0.6987 (t70) REVERT: I 47 ASP cc_start: 0.8890 (p0) cc_final: 0.8036 (p0) REVERT: I 55 ASN cc_start: 0.9162 (t0) cc_final: 0.8898 (t0) REVERT: I 152 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8750 (mt) REVERT: I 161 PHE cc_start: 0.8752 (m-80) cc_final: 0.8545 (m-80) REVERT: J 3 ASP cc_start: 0.7553 (t0) cc_final: 0.6859 (t70) REVERT: J 47 ASP cc_start: 0.9096 (p0) cc_final: 0.8202 (p0) REVERT: J 55 ASN cc_start: 0.9158 (t0) cc_final: 0.8928 (t0) REVERT: J 213 MET cc_start: 0.8273 (mmm) cc_final: 0.7412 (mmm) REVERT: K 3 ASP cc_start: 0.7599 (t0) cc_final: 0.7266 (t70) REVERT: K 47 ASP cc_start: 0.9095 (p0) cc_final: 0.8288 (p0) REVERT: K 55 ASN cc_start: 0.9190 (t0) cc_final: 0.8742 (t0) REVERT: K 213 MET cc_start: 0.8374 (mmm) cc_final: 0.7368 (mmm) REVERT: L 3 ASP cc_start: 0.7720 (t0) cc_final: 0.7087 (t70) REVERT: L 47 ASP cc_start: 0.9128 (p0) cc_final: 0.8520 (p0) REVERT: L 55 ASN cc_start: 0.9164 (t0) cc_final: 0.8907 (t0) REVERT: L 103 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8973 (mt-10) REVERT: L 213 MET cc_start: 0.8332 (mmm) cc_final: 0.7128 (mmm) outliers start: 58 outliers final: 41 residues processed: 522 average time/residue: 0.3194 time to fit residues: 255.8211 Evaluate side-chains 539 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 496 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 187 CYS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 209 optimal weight: 0.0980 chunk 180 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 81 GLN ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21204 Z= 0.137 Angle : 0.552 12.888 28056 Z= 0.269 Chirality : 0.038 0.173 3024 Planarity : 0.003 0.037 3204 Dihedral : 8.370 59.842 3852 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.05 % Allowed : 26.43 % Favored : 71.52 % 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: 1.01 (0.17), residues: 2304 helix: 1.89 (0.13), residues: 1476 sheet: 0.72 (0.43), residues: 132 loop : -2.14 (0.19), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP G 45 HIS 0.002 0.000 HIS J 95 PHE 0.033 0.001 PHE H 30 TYR 0.026 0.001 TYR H 155 ARG 0.003 0.000 ARG F 53 ********************** 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 591 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 548 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7490 (t0) cc_final: 0.6823 (t70) REVERT: A 47 ASP cc_start: 0.9080 (p0) cc_final: 0.8313 (p0) REVERT: A 55 ASN cc_start: 0.9095 (t0) cc_final: 0.8647 (t0) REVERT: A 161 PHE cc_start: 0.8645 (m-80) cc_final: 0.8426 (m-80) REVERT: A 213 MET cc_start: 0.8383 (mmm) cc_final: 0.7228 (mmm) REVERT: B 3 ASP cc_start: 0.7471 (t0) cc_final: 0.6770 (t70) REVERT: B 47 ASP cc_start: 0.9061 (p0) cc_final: 0.8281 (p0) REVERT: B 55 ASN cc_start: 0.9033 (t0) cc_final: 0.8719 (t0) REVERT: B 103 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8978 (mt-10) REVERT: B 213 MET cc_start: 0.8326 (mmm) cc_final: 0.7274 (mmm) REVERT: C 3 ASP cc_start: 0.7547 (t0) cc_final: 0.6801 (t70) REVERT: C 47 ASP cc_start: 0.8999 (p0) cc_final: 0.8258 (p0) REVERT: C 55 ASN cc_start: 0.9008 (t0) cc_final: 0.8725 (t0) REVERT: C 152 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8723 (mt) REVERT: C 213 MET cc_start: 0.8333 (mmm) cc_final: 0.7257 (mmm) REVERT: D 3 ASP cc_start: 0.7492 (t0) cc_final: 0.6821 (t70) REVERT: D 47 ASP cc_start: 0.9019 (p0) cc_final: 0.8330 (p0) REVERT: D 55 ASN cc_start: 0.9072 (t0) cc_final: 0.8859 (t0) REVERT: D 161 PHE cc_start: 0.8645 (m-80) cc_final: 0.8416 (m-80) REVERT: D 213 MET cc_start: 0.8366 (mmm) cc_final: 0.7197 (mmm) REVERT: E 3 ASP cc_start: 0.7592 (t0) cc_final: 0.6859 (t70) REVERT: E 47 ASP cc_start: 0.8930 (p0) cc_final: 0.8375 (p0) REVERT: E 55 ASN cc_start: 0.9034 (t0) cc_final: 0.8714 (t0) REVERT: E 103 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8927 (mt-10) REVERT: E 162 LYS cc_start: 0.7451 (mtpt) cc_final: 0.7154 (mtpp) REVERT: E 213 MET cc_start: 0.8419 (mmm) cc_final: 0.7397 (mmm) REVERT: F 3 ASP cc_start: 0.7470 (t0) cc_final: 0.6760 (t70) REVERT: F 47 ASP cc_start: 0.8994 (p0) cc_final: 0.8230 (p0) REVERT: F 55 ASN cc_start: 0.9071 (t0) cc_final: 0.8850 (t0) REVERT: F 162 LYS cc_start: 0.7386 (mtpt) cc_final: 0.7100 (mtpp) REVERT: F 213 MET cc_start: 0.8438 (mmm) cc_final: 0.7389 (mmm) REVERT: G 3 ASP cc_start: 0.7442 (t0) cc_final: 0.6858 (t70) REVERT: G 47 ASP cc_start: 0.8969 (p0) cc_final: 0.8209 (p0) REVERT: G 55 ASN cc_start: 0.9032 (t0) cc_final: 0.8780 (t0) REVERT: G 103 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8947 (mt-10) REVERT: G 152 LEU cc_start: 0.9401 (tp) cc_final: 0.9054 (mt) REVERT: H 3 ASP cc_start: 0.7467 (t0) cc_final: 0.6877 (t70) REVERT: H 47 ASP cc_start: 0.9040 (p0) cc_final: 0.8286 (p0) REVERT: H 55 ASN cc_start: 0.9067 (t0) cc_final: 0.8829 (t0) REVERT: H 153 ARG cc_start: 0.7859 (mmt180) cc_final: 0.7622 (tpt170) REVERT: I 3 ASP cc_start: 0.7597 (t0) cc_final: 0.6826 (t70) REVERT: I 47 ASP cc_start: 0.8818 (p0) cc_final: 0.8044 (p0) REVERT: I 55 ASN cc_start: 0.9063 (t0) cc_final: 0.8746 (t0) REVERT: I 152 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8716 (mt) REVERT: I 162 LYS cc_start: 0.7502 (mtpt) cc_final: 0.7230 (mtpp) REVERT: J 3 ASP cc_start: 0.7461 (t0) cc_final: 0.6716 (t70) REVERT: J 47 ASP cc_start: 0.9011 (p0) cc_final: 0.8264 (p0) REVERT: J 55 ASN cc_start: 0.9045 (t0) cc_final: 0.8784 (t0) REVERT: J 213 MET cc_start: 0.8275 (mmm) cc_final: 0.7362 (mmm) REVERT: K 3 ASP cc_start: 0.7431 (t0) cc_final: 0.6907 (t70) REVERT: K 47 ASP cc_start: 0.9013 (p0) cc_final: 0.8346 (p0) REVERT: K 55 ASN cc_start: 0.9056 (t0) cc_final: 0.8817 (t0) REVERT: K 166 GLU cc_start: 0.8578 (tp30) cc_final: 0.8370 (tp30) REVERT: K 213 MET cc_start: 0.8374 (mmm) cc_final: 0.7289 (mmm) REVERT: L 3 ASP cc_start: 0.7555 (t0) cc_final: 0.6849 (t70) REVERT: L 47 ASP cc_start: 0.9065 (p0) cc_final: 0.8300 (p0) REVERT: L 55 ASN cc_start: 0.9052 (t0) cc_final: 0.8742 (t0) REVERT: L 103 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8965 (mt-10) outliers start: 43 outliers final: 36 residues processed: 557 average time/residue: 0.3357 time to fit residues: 283.9061 Evaluate side-chains 569 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 531 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 187 CYS Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113757 restraints weight = 34923.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117375 restraints weight = 14263.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119703 restraints weight = 7665.937| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21204 Z= 0.147 Angle : 0.552 12.333 28056 Z= 0.269 Chirality : 0.038 0.191 3024 Planarity : 0.003 0.037 3204 Dihedral : 8.038 56.600 3852 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.05 % Allowed : 26.67 % Favored : 71.29 % 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: 1.02 (0.17), residues: 2304 helix: 1.89 (0.13), residues: 1476 sheet: 0.64 (0.43), residues: 132 loop : -2.09 (0.18), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP G 45 HIS 0.003 0.000 HIS J 95 PHE 0.033 0.001 PHE H 30 TYR 0.023 0.001 TYR H 155 ARG 0.004 0.000 ARG F 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5643.81 seconds wall clock time: 103 minutes 15.46 seconds (6195.46 seconds total)