Starting phenix.real_space_refine on Fri Nov 17 23:11:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/11_2023/7f93_31496_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/11_2023/7f93_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_31496/11_2023/7f93_31496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/11_2023/7f93_31496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/11_2023/7f93_31496_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f93_31496/11_2023/7f93_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-1.21rc1-5144/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: 10.36, 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: 7.53 Conformation dependent library (CDL) restraints added in 3.3 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: 3.56 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: 5.49 Time building geometry restraints manager: 8.15 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: 6.440 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: 28.520 Check model and map are aligned: 0.410 Set scattering table: 0.190 Process input model: 51.420 Find NCS groups from input model: 1.580 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.630 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 43 residues processed: 609 average time/residue: 0.3425 time to fit residues: 309.6158 Evaluate side-chains 502 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 459 time to evaluate : 2.440 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.1760 time to fit residues: 17.4833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 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: 0.8980 chunk 108 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 55 ASN F 58 GLN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 55 ASN G 58 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN H 55 ASN 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 55 ASN 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 55 ASN L 58 GLN L 81 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21204 Z= 0.181 Angle : 0.582 9.120 28056 Z= 0.293 Chirality : 0.037 0.202 3024 Planarity : 0.005 0.038 3204 Dihedral : 10.143 59.217 3852 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.29 % Allowed : 17.43 % 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: -2.17 (0.15), residues: 2304 helix: -0.93 (0.11), residues: 1524 sheet: 0.97 (0.45), residues: 132 loop : -2.97 (0.21), residues: 648 *********************** 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 573 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 525 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 30 residues processed: 532 average time/residue: 0.3425 time to fit residues: 273.8529 Evaluate side-chains 508 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 478 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2016 time to fit residues: 14.2269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 172 optimal weight: 0.0670 chunk 140 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 166 optimal weight: 0.1980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 81 GLN D 81 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN L 224 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2796 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= 0.132 Angle : 0.526 9.014 28056 Z= 0.255 Chirality : 0.036 0.155 3024 Planarity : 0.004 0.031 3204 Dihedral : 9.059 57.886 3852 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.43 % Allowed : 20.24 % Favored : 78.33 % 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: -0.63 (0.17), residues: 2304 helix: 0.48 (0.13), residues: 1524 sheet: 0.49 (0.42), residues: 132 loop : -2.75 (0.21), residues: 648 *********************** 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 552 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 522 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 526 average time/residue: 0.3328 time to fit residues: 267.8095 Evaluate side-chains 491 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 475 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2044 time to fit residues: 8.9256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 D 55 ASN ** 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 63 ASN J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21204 Z= 0.254 Angle : 0.581 8.955 28056 Z= 0.288 Chirality : 0.039 0.132 3024 Planarity : 0.004 0.039 3204 Dihedral : 9.517 57.884 3852 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.86 % Allowed : 23.10 % Favored : 74.05 % 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: 0.26 (0.18), residues: 2304 helix: 1.25 (0.14), residues: 1476 sheet: 0.68 (0.43), residues: 132 loop : -2.38 (0.21), residues: 696 *********************** 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 558 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 498 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 35 residues processed: 524 average time/residue: 0.3091 time to fit residues: 249.8880 Evaluate side-chains 510 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 475 time to evaluate : 2.349 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1954 time to fit residues: 16.1122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 55 ASN C 81 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 55 ASN F 81 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 81 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 ASN J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21204 Z= 0.160 Angle : 0.525 9.863 28056 Z= 0.256 Chirality : 0.037 0.128 3024 Planarity : 0.003 0.037 3204 Dihedral : 8.862 59.951 3852 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.67 % Allowed : 23.90 % Favored : 74.43 % 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: 0.89 (0.18), residues: 2304 helix: 1.63 (0.14), residues: 1488 sheet: 0.45 (0.42), residues: 132 loop : -1.79 (0.23), residues: 684 *********************** 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 555 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 520 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 538 average time/residue: 0.3249 time to fit residues: 267.9542 Evaluate side-chains 499 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 481 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1960 time to fit residues: 9.5968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 18 optimal weight: 0.0770 chunk 72 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 overall best weight: 1.1740 ------------------------------------------------------------------------------- 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 ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN 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 224 ASN J 81 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21204 Z= 0.157 Angle : 0.540 10.613 28056 Z= 0.264 Chirality : 0.038 0.160 3024 Planarity : 0.003 0.036 3204 Dihedral : 8.693 59.827 3852 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.76 % Allowed : 24.86 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2304 helix: 1.84 (0.13), residues: 1488 sheet: 0.47 (0.42), residues: 132 loop : -1.70 (0.23), residues: 684 *********************** 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 564 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 527 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 537 average time/residue: 0.3383 time to fit residues: 276.4093 Evaluate side-chains 503 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 486 time to evaluate : 2.298 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2014 time to fit residues: 9.2028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 0.0170 chunk 123 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- 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 ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3546 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= 0.153 Angle : 0.538 10.265 28056 Z= 0.261 Chirality : 0.038 0.185 3024 Planarity : 0.003 0.036 3204 Dihedral : 8.471 59.998 3852 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.10 % Allowed : 26.19 % Favored : 72.71 % 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: 1.24 (0.17), residues: 2304 helix: 1.89 (0.13), residues: 1488 sheet: 0.56 (0.42), residues: 132 loop : -1.61 (0.22), residues: 684 *********************** 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 547 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 524 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 532 average time/residue: 0.3257 time to fit residues: 265.5665 Evaluate side-chains 506 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 491 time to evaluate : 2.269 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1928 time to fit residues: 8.4055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 172 optimal weight: 0.4980 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 55 ASN C 81 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN F 63 ASN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 ASN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21204 Z= 0.223 Angle : 0.575 10.629 28056 Z= 0.285 Chirality : 0.040 0.175 3024 Planarity : 0.004 0.037 3204 Dihedral : 8.778 59.995 3852 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.24 % Allowed : 27.14 % Favored : 71.62 % 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: 1.31 (0.18), residues: 2304 helix: 1.93 (0.13), residues: 1488 sheet: 0.54 (0.42), residues: 132 loop : -1.52 (0.23), residues: 684 *********************** 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 522 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 496 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 508 average time/residue: 0.3307 time to fit residues: 257.2810 Evaluate side-chains 496 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 477 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1826 time to fit residues: 9.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 193 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21204 Z= 0.159 Angle : 0.553 11.206 28056 Z= 0.273 Chirality : 0.039 0.172 3024 Planarity : 0.003 0.037 3204 Dihedral : 8.353 59.338 3852 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.48 % Allowed : 27.76 % Favored : 71.76 % 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: 1.37 (0.18), residues: 2304 helix: 1.98 (0.13), residues: 1488 sheet: 0.65 (0.43), residues: 132 loop : -1.52 (0.23), residues: 684 *********************** 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 534 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 524 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 529 average time/residue: 0.3278 time to fit residues: 265.5871 Evaluate side-chains 501 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 496 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2034 time to fit residues: 4.7423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 209 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 55 ASN C 81 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 ASN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21204 Z= 0.175 Angle : 0.568 11.325 28056 Z= 0.282 Chirality : 0.040 0.170 3024 Planarity : 0.004 0.037 3204 Dihedral : 8.281 57.637 3852 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.67 % Allowed : 28.71 % Favored : 70.62 % 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: 1.20 (0.17), residues: 2304 helix: 1.91 (0.13), residues: 1500 sheet: 0.67 (0.43), residues: 132 loop : -1.87 (0.20), residues: 672 ********************** 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 523 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 509 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 516 average time/residue: 0.3286 time to fit residues: 257.8685 Evaluate side-chains 497 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 490 time to evaluate : 2.348 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1897 time to fit residues: 5.5124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118060 restraints weight = 34525.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121741 restraints weight = 14111.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124081 restraints weight = 7556.855| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21204 Z= 0.157 Angle : 0.565 11.254 28056 Z= 0.279 Chirality : 0.040 0.167 3024 Planarity : 0.003 0.037 3204 Dihedral : 7.970 56.569 3852 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.24 % Allowed : 29.29 % Favored : 70.48 % 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: 1.20 (0.17), residues: 2304 helix: 1.91 (0.13), residues: 1500 sheet: 0.70 (0.43), residues: 132 loop : -1.88 (0.20), residues: 672 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5455.92 seconds wall clock time: 99 minutes 41.71 seconds (5981.71 seconds total)