Starting phenix.real_space_refine on Fri Mar 6 19:29:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lf2_23298/03_2026/7lf2_23298.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lf2_23298/03_2026/7lf2_23298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lf2_23298/03_2026/7lf2_23298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lf2_23298/03_2026/7lf2_23298.map" model { file = "/net/cci-nas-00/data/ceres_data/7lf2_23298/03_2026/7lf2_23298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lf2_23298/03_2026/7lf2_23298.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.062 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: 5 Type Number sf(0) Gaussians Mn 12 7.51 5 S 108 5.16 5 C 21408 2.51 5 N 5640 2.21 5 O 6630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33798 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "D" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "J" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "K" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "R" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "I" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.60, per 1000 atoms: 0.22 Number of scatterers: 33798 At special positions: 0 Unit cell: (131.04, 125.84, 210.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 12 24.99 S 108 16.00 O 6630 8.00 N 5640 7.00 C 21408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 143 " - pdb=" SG CYS D 199 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 143 " - pdb=" SG CYS G 199 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 143 " - pdb=" SG CYS F 199 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 143 " - pdb=" SG CYS K 199 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 143 " - pdb=" SG CYS O 199 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 143 " - pdb=" SG CYS P 199 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.6 seconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8112 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 60 sheets defined 21.8% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.784A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.542A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.880A pdb=" N LEU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 207 through 221 Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.651A pdb=" N GLY A 268 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.529A pdb=" N GLY A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 303 removed outlier: 3.579A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.715A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.732A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 207 through 221 Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.620A pdb=" N GLY B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.532A pdb=" N GLY B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 303 removed outlier: 3.513A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 3.724A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 removed outlier: 4.473A pdb=" N GLY C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.828A pdb=" N LEU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 199 through 207 Processing helix chain 'C' and resid 207 through 221 Processing helix chain 'C' and resid 253 through 268 removed outlier: 3.596A pdb=" N GLY C 268 " --> pdb=" O ILE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.515A pdb=" N GLY C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 303 removed outlier: 3.542A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 26 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 36 through 41 Processing helix chain 'J' and resid 69 through 90 removed outlier: 3.992A pdb=" N VAL J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN J 90 " --> pdb=" O GLU J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.697A pdb=" N HIS J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL J 114 " --> pdb=" O GLY J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.947A pdb=" N LEU J 148 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 183 through 194 removed outlier: 3.543A pdb=" N GLY J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 207 Processing helix chain 'J' and resid 207 through 220 Processing helix chain 'J' and resid 253 through 268 removed outlier: 3.811A pdb=" N GLY J 268 " --> pdb=" O ILE J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 283 removed outlier: 3.868A pdb=" N GLY J 283 " --> pdb=" O PRO J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 303 removed outlier: 3.642A pdb=" N VAL J 289 " --> pdb=" O THR J 285 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 26 Processing helix chain 'Q' and resid 27 through 34 Processing helix chain 'Q' and resid 36 through 41 Processing helix chain 'Q' and resid 69 through 90 removed outlier: 3.979A pdb=" N VAL Q 73 " --> pdb=" O ASN Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 102 No H-bonds generated for 'chain 'Q' and resid 100 through 102' Processing helix chain 'Q' and resid 103 through 115 removed outlier: 3.686A pdb=" N HIS Q 111 " --> pdb=" O SER Q 107 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL Q 114 " --> pdb=" O GLY Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 149 removed outlier: 3.922A pdb=" N LEU Q 148 " --> pdb=" O PRO Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 153 Processing helix chain 'Q' and resid 183 through 194 removed outlier: 3.551A pdb=" N GLY Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 200 through 207 Processing helix chain 'Q' and resid 207 through 220 Processing helix chain 'Q' and resid 253 through 268 removed outlier: 3.825A pdb=" N GLY Q 268 " --> pdb=" O ILE Q 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 283 removed outlier: 3.811A pdb=" N GLY Q 283 " --> pdb=" O PRO Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 285 through 303 removed outlier: 3.671A pdb=" N VAL Q 289 " --> pdb=" O THR Q 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 26 Processing helix chain 'R' and resid 27 through 34 Processing helix chain 'R' and resid 36 through 41 Processing helix chain 'R' and resid 69 through 90 removed outlier: 3.942A pdb=" N VAL R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 102 No H-bonds generated for 'chain 'R' and resid 100 through 102' Processing helix chain 'R' and resid 103 through 115 removed outlier: 3.687A pdb=" N HIS R 111 " --> pdb=" O SER R 107 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL R 114 " --> pdb=" O GLY R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 149 removed outlier: 3.933A pdb=" N LEU R 148 " --> pdb=" O PRO R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 153 Processing helix chain 'R' and resid 183 through 194 removed outlier: 3.577A pdb=" N GLY R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 207 Processing helix chain 'R' and resid 207 through 220 Processing helix chain 'R' and resid 253 through 268 removed outlier: 3.810A pdb=" N GLY R 268 " --> pdb=" O ILE R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 283 removed outlier: 3.885A pdb=" N GLY R 283 " --> pdb=" O PRO R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 303 removed outlier: 3.620A pdb=" N VAL R 289 " --> pdb=" O THR R 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.715A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.715A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 126 Processing helix chain 'M' and resid 183 through 188 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 126 Processing helix chain 'N' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 52 removed outlier: 6.392A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR A 50 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE A 10 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP A 52 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 12 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 272 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 120 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE A 177 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP A 122 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR A 176 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 11 removed outlier: 7.025A pdb=" N GLU D 10 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 141 through 148 removed outlier: 3.553A pdb=" N VAL D 184 " --> pdb=" O CYS D 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 147 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER D 180 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 200 through 203 Processing sheet with id=AA6, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'E' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.922A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 154 through 155 removed outlier: 4.451A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 11 removed outlier: 7.026A pdb=" N GLU G 10 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 141 through 148 removed outlier: 3.552A pdb=" N VAL G 184 " --> pdb=" O CYS G 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP G 147 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER G 180 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 200 through 203 Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.026A pdb=" N GLU F 10 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 141 through 148 removed outlier: 3.554A pdb=" N VAL F 184 " --> pdb=" O CYS F 143 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP F 147 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER F 180 " --> pdb=" O ASP F 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 200 through 203 Processing sheet with id=AC1, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.228A pdb=" N GLY B 12 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP B 52 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY B 272 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 120 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 177 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP B 122 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.195A pdb=" N GLY C 12 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP C 52 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY C 272 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 120 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE C 177 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP C 122 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 46 through 52 removed outlier: 6.717A pdb=" N GLY J 12 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP J 52 " --> pdb=" O GLY J 12 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE J 227 " --> pdb=" O LEU J 270 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY J 272 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.025A pdb=" N GLU K 10 " --> pdb=" O THR K 113 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 141 through 148 removed outlier: 3.552A pdb=" N VAL K 184 " --> pdb=" O CYS K 143 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP K 147 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER K 180 " --> pdb=" O ASP K 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 200 through 203 Processing sheet with id=AC8, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.025A pdb=" N GLU O 10 " --> pdb=" O THR O 113 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 141 through 148 removed outlier: 3.553A pdb=" N VAL O 184 " --> pdb=" O CYS O 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP O 147 " --> pdb=" O SER O 180 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER O 180 " --> pdb=" O ASP O 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 200 through 203 Processing sheet with id=AD3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'P' and resid 10 through 11 removed outlier: 7.024A pdb=" N GLU P 10 " --> pdb=" O THR P 113 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET P 34 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 141 through 148 removed outlier: 3.553A pdb=" N VAL P 184 " --> pdb=" O CYS P 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP P 147 " --> pdb=" O SER P 180 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER P 180 " --> pdb=" O ASP P 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 200 through 203 Processing sheet with id=AD7, first strand: chain 'Q' and resid 46 through 52 removed outlier: 6.735A pdb=" N GLY Q 12 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP Q 52 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE Q 227 " --> pdb=" O LEU Q 270 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY Q 272 " --> pdb=" O ILE Q 227 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY Q 119 " --> pdb=" O HIS Q 228 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER Q 230 " --> pdb=" O GLY Q 119 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE Q 121 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP Q 232 " --> pdb=" O ILE Q 121 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL Q 123 " --> pdb=" O ASP Q 232 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 46 through 52 removed outlier: 6.761A pdb=" N GLY R 12 " --> pdb=" O TYR R 50 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP R 52 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE R 227 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY R 272 " --> pdb=" O ILE R 227 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLY R 119 " --> pdb=" O HIS R 228 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER R 230 " --> pdb=" O GLY R 119 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE R 121 " --> pdb=" O SER R 230 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP R 232 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL R 123 " --> pdb=" O ASP R 232 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AE2, first strand: chain 'I' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 114 through 118 removed outlier: 5.923A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 154 through 155 removed outlier: 4.450A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE7, first strand: chain 'H' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.922A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 154 through 155 removed outlier: 4.451A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AF3, first strand: chain 'L' and resid 46 through 48 removed outlier: 6.359A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.923A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.452A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AF7, first strand: chain 'M' and resid 10 through 13 Processing sheet with id=AF8, first strand: chain 'M' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 114 through 118 removed outlier: 5.921A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 154 through 155 removed outlier: 4.452A pdb=" N TRP M 148 " --> pdb=" O GLN M 155 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AG3, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AG4, first strand: chain 'N' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 114 through 118 removed outlier: 5.923A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 154 through 155 removed outlier: 4.451A pdb=" N TRP N 148 " --> pdb=" O GLN N 155 " (cutoff:3.500A) 1157 hydrogen bonds defined for protein. 3120 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: 7.05 Time building geometry restraints manager: 3.88 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: 10530 1.34 - 1.45: 6384 1.45 - 1.57: 17478 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 34530 Sorted by residual: bond pdb=" CA SER D 176 " pdb=" CB SER D 176 " ideal model delta sigma weight residual 1.532 1.498 0.034 1.28e-02 6.10e+03 7.01e+00 bond pdb=" CA SER G 176 " pdb=" CB SER G 176 " ideal model delta sigma weight residual 1.532 1.499 0.034 1.28e-02 6.10e+03 6.91e+00 bond pdb=" CA SER K 176 " pdb=" CB SER K 176 " ideal model delta sigma weight residual 1.532 1.499 0.034 1.28e-02 6.10e+03 6.91e+00 bond pdb=" CA SER P 176 " pdb=" CB SER P 176 " ideal model delta sigma weight residual 1.532 1.499 0.034 1.28e-02 6.10e+03 6.88e+00 bond pdb=" CA SER O 176 " pdb=" CB SER O 176 " ideal model delta sigma weight residual 1.532 1.499 0.033 1.28e-02 6.10e+03 6.70e+00 ... (remaining 34525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 45249 2.43 - 4.87: 1393 4.87 - 7.30: 225 7.30 - 9.73: 70 9.73 - 12.17: 7 Bond angle restraints: 46944 Sorted by residual: angle pdb=" N ILE C 66 " pdb=" CA ILE C 66 " pdb=" C ILE C 66 " ideal model delta sigma weight residual 111.81 106.92 4.89 8.60e-01 1.35e+00 3.23e+01 angle pdb=" N ILE B 66 " pdb=" CA ILE B 66 " pdb=" C ILE B 66 " ideal model delta sigma weight residual 111.81 107.10 4.71 8.60e-01 1.35e+00 2.99e+01 angle pdb=" N ILE A 66 " pdb=" CA ILE A 66 " pdb=" C ILE A 66 " ideal model delta sigma weight residual 111.81 107.15 4.66 8.60e-01 1.35e+00 2.94e+01 angle pdb=" N GLN C 143 " pdb=" CA GLN C 143 " pdb=" C GLN C 143 " ideal model delta sigma weight residual 109.81 119.52 -9.71 2.21e+00 2.05e-01 1.93e+01 angle pdb=" N GLN A 143 " pdb=" CA GLN A 143 " pdb=" C GLN A 143 " ideal model delta sigma weight residual 109.81 119.49 -9.68 2.21e+00 2.05e-01 1.92e+01 ... (remaining 46939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 19602 14.11 - 28.21: 800 28.21 - 42.32: 214 42.32 - 56.43: 42 56.43 - 70.53: 6 Dihedral angle restraints: 20664 sinusoidal: 7944 harmonic: 12720 Sorted by residual: dihedral pdb=" CA GLN H 53 " pdb=" C GLN H 53 " pdb=" N SER H 54 " pdb=" CA SER H 54 " ideal model delta harmonic sigma weight residual 180.00 127.90 52.10 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA GLN N 53 " pdb=" C GLN N 53 " pdb=" N SER N 54 " pdb=" CA SER N 54 " ideal model delta harmonic sigma weight residual 180.00 127.92 52.08 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA GLN I 53 " pdb=" C GLN I 53 " pdb=" N SER I 54 " pdb=" CA SER I 54 " ideal model delta harmonic sigma weight residual 180.00 127.94 52.06 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 20661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4599 0.082 - 0.165: 692 0.165 - 0.247: 66 0.247 - 0.329: 7 0.329 - 0.412: 6 Chirality restraints: 5370 Sorted by residual: chirality pdb=" CB ILE N 58 " pdb=" CA ILE N 58 " pdb=" CG1 ILE N 58 " pdb=" CG2 ILE N 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB ILE I 58 " pdb=" CA ILE I 58 " pdb=" CG1 ILE I 58 " pdb=" CG2 ILE I 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE E 58 " pdb=" CA ILE E 58 " pdb=" CG1 ILE E 58 " pdb=" CG2 ILE E 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.20e+00 ... (remaining 5367 not shown) Planarity restraints: 5994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP E 94 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.87e+00 pdb=" N PRO E 95 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP I 94 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO I 95 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO I 95 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 95 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 94 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO L 95 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.037 5.00e-02 4.00e+02 ... (remaining 5991 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.66: 3 1.66 - 2.47: 261 2.47 - 3.28: 37225 3.28 - 4.09: 92003 4.09 - 4.90: 161858 Warning: very small nonbonded interaction distances. Nonbonded interactions: 291350 Sorted by model distance: nonbonded pdb="MN MN C1001 " pdb="MN MN C1002 " model vdw 0.855 1.600 nonbonded pdb="MN MN A1001 " pdb="MN MN A1002 " model vdw 0.856 1.600 nonbonded pdb="MN MN B1001 " pdb="MN MN B1002 " model vdw 0.869 1.600 nonbonded pdb=" OD2 ASP C 232 " pdb="MN MN C1002 " model vdw 1.848 2.320 nonbonded pdb=" OD2 ASP B 232 " pdb="MN MN B1002 " model vdw 1.861 2.320 ... (remaining 291345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 31.190 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 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 0.093 34554 Z= 0.325 Angle : 1.034 12.166 46992 Z= 0.550 Chirality : 0.058 0.412 5370 Planarity : 0.009 0.070 5994 Dihedral : 9.005 70.533 12480 Min Nonbonded Distance : 0.855 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.01 % Favored : 88.85 % Rotamer: Outliers : 0.16 % Allowed : 2.39 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.11), residues: 4368 helix: -2.31 (0.14), residues: 828 sheet: -3.10 (0.12), residues: 1326 loop : -2.52 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 180 TYR 0.029 0.003 TYR B 254 PHE 0.025 0.003 PHE D 169 TRP 0.017 0.003 TRP D 47 HIS 0.012 0.003 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00698 (34530) covalent geometry : angle 1.03353 (46944) SS BOND : bond 0.00641 ( 24) SS BOND : angle 1.36382 ( 48) hydrogen bonds : bond 0.24423 ( 1157) hydrogen bonds : angle 10.75249 ( 3120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 542 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7984 (t0) cc_final: 0.7632 (t0) REVERT: A 200 MET cc_start: 0.8466 (mmm) cc_final: 0.7980 (mmm) REVERT: D 97 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8065 (t) REVERT: E 32 ASP cc_start: 0.8024 (m-30) cc_final: 0.7798 (m-30) REVERT: E 49 LYS cc_start: 0.8357 (mttt) cc_final: 0.8008 (mtpt) REVERT: B 46 ASP cc_start: 0.7763 (t0) cc_final: 0.7463 (t0) REVERT: C 146 SER cc_start: 0.8782 (p) cc_final: 0.8566 (t) REVERT: J 95 LEU cc_start: 0.9031 (tp) cc_final: 0.8709 (mt) REVERT: J 111 HIS cc_start: 0.5808 (t-170) cc_final: 0.5238 (t-170) REVERT: J 122 TRP cc_start: 0.5148 (t-100) cc_final: 0.4831 (t-100) REVERT: J 143 GLN cc_start: 0.5599 (mt0) cc_final: 0.5174 (mp10) REVERT: J 237 ASP cc_start: 0.9500 (t70) cc_final: 0.9149 (p0) REVERT: J 279 ASN cc_start: 0.6790 (t0) cc_final: 0.5998 (t0) REVERT: J 292 THR cc_start: 0.8183 (m) cc_final: 0.7964 (p) REVERT: K 36 TRP cc_start: 0.2285 (m100) cc_final: 0.1559 (m-10) REVERT: K 58 THR cc_start: 0.9290 (p) cc_final: 0.9029 (p) REVERT: K 64 PHE cc_start: 0.5545 (m-10) cc_final: 0.5242 (m-10) REVERT: K 97 VAL cc_start: 0.6352 (OUTLIER) cc_final: 0.5680 (t) REVERT: K 101 TYR cc_start: 0.7473 (m-80) cc_final: 0.7147 (m-80) REVERT: K 103 PHE cc_start: 0.4460 (m-10) cc_final: 0.4236 (m-10) REVERT: K 212 LYS cc_start: 0.6038 (mmtt) cc_final: 0.5671 (mmmt) REVERT: O 58 THR cc_start: 0.9154 (p) cc_final: 0.8928 (p) REVERT: O 63 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8571 (pttm) REVERT: O 81 MET cc_start: 0.3238 (ttp) cc_final: 0.2648 (ttp) REVERT: O 97 VAL cc_start: 0.5330 (OUTLIER) cc_final: 0.4561 (t) REVERT: O 101 TYR cc_start: 0.7817 (m-80) cc_final: 0.7335 (m-80) REVERT: O 195 LYS cc_start: 0.5408 (mttt) cc_final: 0.5207 (mptt) REVERT: P 81 MET cc_start: 0.4585 (ttp) cc_final: 0.3799 (tmm) REVERT: P 97 VAL cc_start: 0.5395 (OUTLIER) cc_final: 0.4387 (t) REVERT: Q 95 LEU cc_start: 0.8736 (tp) cc_final: 0.8203 (mm) REVERT: Q 111 HIS cc_start: 0.4896 (t-170) cc_final: 0.4445 (t-170) REVERT: Q 122 TRP cc_start: 0.4074 (t-100) cc_final: 0.3645 (t-100) REVERT: Q 172 LYS cc_start: 0.4204 (pttm) cc_final: 0.3930 (mmtm) REVERT: Q 237 ASP cc_start: 0.9407 (t70) cc_final: 0.9113 (p0) REVERT: Q 279 ASN cc_start: 0.6877 (t0) cc_final: 0.6472 (t0) REVERT: Q 292 THR cc_start: 0.8309 (m) cc_final: 0.7896 (m) REVERT: R 95 LEU cc_start: 0.8818 (tp) cc_final: 0.8488 (mt) REVERT: R 111 HIS cc_start: 0.5557 (t-170) cc_final: 0.5270 (t-170) REVERT: R 172 LYS cc_start: 0.4757 (pttm) cc_final: 0.4389 (mmmt) REVERT: R 237 ASP cc_start: 0.9275 (t70) cc_final: 0.8994 (p0) REVERT: R 279 ASN cc_start: 0.6538 (t0) cc_final: 0.6028 (t0) REVERT: I 49 LYS cc_start: 0.8341 (mttt) cc_final: 0.8135 (mttt) REVERT: H 32 ASP cc_start: 0.7478 (m-30) cc_final: 0.7274 (m-30) REVERT: L 11 LEU cc_start: 0.5441 (tm) cc_final: 0.5092 (tt) REVERT: L 38 GLN cc_start: 0.8065 (tt0) cc_final: 0.7852 (tm-30) REVERT: L 123 GLU cc_start: 0.3618 (tt0) cc_final: 0.2903 (mm-30) REVERT: L 161 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7111 (tp30) REVERT: M 213 GLU cc_start: 0.2360 (tt0) cc_final: 0.1606 (tm-30) REVERT: N 105 GLU cc_start: 0.5971 (mt-10) cc_final: 0.5590 (mp0) REVERT: N 123 GLU cc_start: 0.3721 (tt0) cc_final: 0.3278 (tt0) REVERT: N 161 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7293 (tp30) outliers start: 6 outliers final: 1 residues processed: 544 average time/residue: 0.2628 time to fit residues: 212.9719 Evaluate side-chains 265 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 260 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 40.0000 chunk 424 optimal weight: 30.0000 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 141 HIS A 319 ASN D 61 ASN D 174 GLN E 92 ASN E 137 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 174 GLN F 61 ASN F 174 GLN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 141 HIS B 319 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS C 141 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS J 143 GLN J 319 ASN K 61 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 HIS O 174 GLN P 61 ASN ** P 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 ASN Q 126 HIS Q 143 GLN Q 294 ASN Q 319 ASN R 90 ASN R 143 GLN R 319 ASN I 92 ASN I 137 ASN ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN H 137 ASN H 160 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN L 160 GLN L 189 HIS M 92 ASN M 137 ASN M 189 HIS N 137 ASN N 160 GLN N 189 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.153479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.109486 restraints weight = 132445.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111033 restraints weight = 67605.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111704 restraints weight = 35881.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111799 restraints weight = 29239.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.111932 restraints weight = 25954.375| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 34554 Z= 0.302 Angle : 0.852 10.830 46992 Z= 0.431 Chirality : 0.050 0.204 5370 Planarity : 0.007 0.119 5994 Dihedral : 7.120 47.304 4757 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.58 % Favored : 89.29 % Rotamer: Outliers : 1.89 % Allowed : 6.41 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.12), residues: 4368 helix: -0.96 (0.17), residues: 834 sheet: -2.82 (0.12), residues: 1344 loop : -2.23 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 180 TYR 0.029 0.003 TYR R 265 PHE 0.033 0.002 PHE B 64 TRP 0.037 0.003 TRP O 36 HIS 0.010 0.002 HIS N 34 Details of bonding type rmsd covalent geometry : bond 0.00681 (34530) covalent geometry : angle 0.85160 (46944) SS BOND : bond 0.00500 ( 24) SS BOND : angle 0.93847 ( 48) hydrogen bonds : bond 0.04393 ( 1157) hydrogen bonds : angle 7.55005 ( 3120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 272 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8866 (tptp) cc_final: 0.8630 (tptp) REVERT: A 46 ASP cc_start: 0.8370 (t0) cc_final: 0.8053 (t0) REVERT: A 97 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8367 (pp) REVERT: A 200 MET cc_start: 0.9124 (mmm) cc_final: 0.8466 (mpp) REVERT: D 97 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9008 (t) REVERT: F 34 MET cc_start: 0.8852 (mmm) cc_final: 0.8515 (tpt) REVERT: F 97 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8747 (t) REVERT: B 46 ASP cc_start: 0.8149 (t0) cc_final: 0.7883 (t0) REVERT: B 97 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8379 (pp) REVERT: B 211 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8501 (p) REVERT: B 212 MET cc_start: 0.9132 (mmm) cc_final: 0.8751 (mmm) REVERT: C 97 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8333 (pp) REVERT: J 95 LEU cc_start: 0.9164 (tp) cc_final: 0.8634 (mm) REVERT: J 122 TRP cc_start: 0.5946 (t-100) cc_final: 0.5694 (t-100) REVERT: J 279 ASN cc_start: 0.7097 (t0) cc_final: 0.6594 (t0) REVERT: O 36 TRP cc_start: 0.6457 (m100) cc_final: 0.6058 (m-10) REVERT: P 36 TRP cc_start: 0.6818 (m100) cc_final: 0.6127 (m100) REVERT: P 204 LYS cc_start: 0.6930 (mmmt) cc_final: 0.6264 (tptm) REVERT: P 209 LYS cc_start: 0.5283 (tptt) cc_final: 0.5008 (tppt) REVERT: Q 95 LEU cc_start: 0.8841 (tp) cc_final: 0.8290 (mm) REVERT: Q 122 TRP cc_start: 0.6012 (t-100) cc_final: 0.5613 (t-100) REVERT: Q 172 LYS cc_start: 0.4225 (pttm) cc_final: 0.3927 (mmtm) REVERT: Q 279 ASN cc_start: 0.7146 (t0) cc_final: 0.6795 (t0) REVERT: R 95 LEU cc_start: 0.8931 (tp) cc_final: 0.8428 (mm) REVERT: R 265 TYR cc_start: 0.4984 (t80) cc_final: 0.4666 (t80) REVERT: L 123 GLU cc_start: 0.2662 (tt0) cc_final: 0.1814 (mm-30) REVERT: L 161 GLU cc_start: 0.7589 (mt-10) cc_final: 0.6899 (tp30) REVERT: N 126 LYS cc_start: 0.4181 (pttt) cc_final: 0.3777 (pttm) REVERT: N 169 LYS cc_start: 0.3725 (pttm) cc_final: 0.3469 (mttt) outliers start: 71 outliers final: 31 residues processed: 330 average time/residue: 0.2254 time to fit residues: 117.8629 Evaluate side-chains 233 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 329 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 308 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 230 optimal weight: 40.0000 chunk 377 optimal weight: 5.9990 chunk 314 optimal weight: 0.0980 chunk 27 optimal weight: 8.9990 chunk 423 optimal weight: 40.0000 chunk 52 optimal weight: 0.5980 chunk 398 optimal weight: 6.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN J 90 ASN K 174 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 GLN R 126 HIS ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN M 92 ASN N 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.152571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107968 restraints weight = 131553.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109605 restraints weight = 63599.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110480 restraints weight = 32124.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110521 restraints weight = 24893.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110607 restraints weight = 22899.292| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 34554 Z= 0.282 Angle : 0.788 10.945 46992 Z= 0.399 Chirality : 0.049 0.196 5370 Planarity : 0.006 0.075 5994 Dihedral : 6.654 45.457 4754 Min Nonbonded Distance : 1.406 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.99 % Favored : 88.87 % Rotamer: Outliers : 2.47 % Allowed : 7.84 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.12), residues: 4368 helix: -0.63 (0.17), residues: 840 sheet: -2.58 (0.13), residues: 1374 loop : -2.03 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 38 TYR 0.020 0.002 TYR J 265 PHE 0.024 0.002 PHE B 64 TRP 0.033 0.002 TRP M 148 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00642 (34530) covalent geometry : angle 0.78855 (46944) SS BOND : bond 0.00364 ( 24) SS BOND : angle 0.73909 ( 48) hydrogen bonds : bond 0.04098 ( 1157) hydrogen bonds : angle 6.91396 ( 3120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 218 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8915 (tptp) cc_final: 0.8672 (tptp) REVERT: A 97 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8437 (pp) REVERT: A 200 MET cc_start: 0.9151 (mmm) cc_final: 0.8373 (mpp) REVERT: D 97 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9072 (m) REVERT: E 108 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7464 (ppp80) REVERT: F 97 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.8804 (t) REVERT: B 97 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8459 (pp) REVERT: B 211 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8467 (p) REVERT: B 212 MET cc_start: 0.9182 (mmm) cc_final: 0.8750 (mmm) REVERT: B 237 ASP cc_start: 0.8608 (t0) cc_final: 0.8370 (t0) REVERT: C 97 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8480 (pp) REVERT: J 95 LEU cc_start: 0.9130 (tp) cc_final: 0.8607 (mm) REVERT: J 265 TYR cc_start: 0.4886 (t80) cc_final: 0.4624 (t80) REVERT: J 279 ASN cc_start: 0.6997 (t0) cc_final: 0.6620 (t0) REVERT: K 38 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7145 (tmm-80) REVERT: P 204 LYS cc_start: 0.7115 (mmmt) cc_final: 0.6386 (tptp) REVERT: P 209 LYS cc_start: 0.5156 (tptt) cc_final: 0.4867 (tppt) REVERT: Q 95 LEU cc_start: 0.8895 (tp) cc_final: 0.8405 (mm) REVERT: Q 172 LYS cc_start: 0.4103 (pttm) cc_final: 0.3795 (mmtm) REVERT: Q 258 LEU cc_start: 0.8871 (mt) cc_final: 0.8588 (tt) REVERT: R 95 LEU cc_start: 0.8955 (tp) cc_final: 0.8437 (mm) REVERT: I 108 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7685 (ppp80) REVERT: L 123 GLU cc_start: 0.2656 (tt0) cc_final: 0.1846 (mm-30) REVERT: L 148 TRP cc_start: 0.3778 (m100) cc_final: 0.3203 (m100) REVERT: L 161 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7048 (tp30) REVERT: L 209 PHE cc_start: 0.2469 (p90) cc_final: 0.2181 (m-10) outliers start: 93 outliers final: 41 residues processed: 297 average time/residue: 0.2194 time to fit residues: 105.0524 Evaluate side-chains 242 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 209 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 410 optimal weight: 7.9990 chunk 407 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 240 optimal weight: 40.0000 chunk 280 optimal weight: 30.0000 chunk 355 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 379 optimal weight: 0.0010 chunk 400 optimal weight: 30.0000 chunk 219 optimal weight: 10.0000 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 HIS ** H 189 HIS ** 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 = 0.4383 r_free = 0.4383 target = 0.153342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.110177 restraints weight = 130250.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111826 restraints weight = 65670.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112444 restraints weight = 33439.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112535 restraints weight = 27818.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112659 restraints weight = 23965.875| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34554 Z= 0.182 Angle : 0.695 10.696 46992 Z= 0.353 Chirality : 0.047 0.219 5370 Planarity : 0.005 0.069 5994 Dihedral : 6.308 43.449 4754 Min Nonbonded Distance : 1.453 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.07 % Favored : 89.79 % Rotamer: Outliers : 2.45 % Allowed : 8.56 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.12), residues: 4368 helix: -0.34 (0.17), residues: 840 sheet: -2.35 (0.12), residues: 1440 loop : -1.92 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 180 TYR 0.021 0.002 TYR Q 265 PHE 0.016 0.001 PHE B 64 TRP 0.043 0.002 TRP O 36 HIS 0.004 0.001 HIS N 34 Details of bonding type rmsd covalent geometry : bond 0.00415 (34530) covalent geometry : angle 0.69568 (46944) SS BOND : bond 0.00268 ( 24) SS BOND : angle 0.47622 ( 48) hydrogen bonds : bond 0.03573 ( 1157) hydrogen bonds : angle 6.45034 ( 3120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 209 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8863 (tptp) cc_final: 0.8618 (tptp) REVERT: A 97 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8440 (pp) REVERT: A 200 MET cc_start: 0.9180 (mmm) cc_final: 0.8538 (mpp) REVERT: E 108 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7597 (ppp80) REVERT: G 173 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8156 (tm) REVERT: F 34 MET cc_start: 0.8941 (mmm) cc_final: 0.8539 (tpt) REVERT: B 6 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7839 (ptp90) REVERT: B 97 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8374 (pp) REVERT: B 212 MET cc_start: 0.9171 (mmm) cc_final: 0.8758 (mmm) REVERT: C 97 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8448 (pp) REVERT: J 95 LEU cc_start: 0.9114 (tp) cc_final: 0.8542 (mm) REVERT: J 97 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6638 (pp) REVERT: J 198 PHE cc_start: 0.8165 (m-80) cc_final: 0.7960 (m-80) REVERT: J 265 TYR cc_start: 0.4874 (t80) cc_final: 0.4591 (t80) REVERT: J 279 ASN cc_start: 0.7347 (t0) cc_final: 0.6992 (t0) REVERT: K 38 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7043 (tmm-80) REVERT: P 157 TRP cc_start: -0.0174 (m100) cc_final: -0.0695 (m100) REVERT: P 204 LYS cc_start: 0.7238 (mmmt) cc_final: 0.6478 (tptp) REVERT: P 209 LYS cc_start: 0.5249 (tptt) cc_final: 0.4895 (tppt) REVERT: Q 95 LEU cc_start: 0.8806 (tp) cc_final: 0.8333 (mp) REVERT: Q 172 LYS cc_start: 0.4243 (pttm) cc_final: 0.3703 (mmtm) REVERT: Q 258 LEU cc_start: 0.8917 (mt) cc_final: 0.8641 (tt) REVERT: Q 290 THR cc_start: 0.8320 (m) cc_final: 0.7970 (m) REVERT: R 95 LEU cc_start: 0.8991 (tp) cc_final: 0.8563 (mp) REVERT: R 197 TYR cc_start: 0.8126 (p90) cc_final: 0.7877 (p90) REVERT: R 291 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7584 (ttp-170) REVERT: I 108 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7707 (ppp80) REVERT: H 108 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7587 (ppp80) REVERT: L 123 GLU cc_start: 0.2494 (tt0) cc_final: 0.1677 (mm-30) REVERT: L 148 TRP cc_start: 0.3612 (m100) cc_final: 0.3127 (m100) REVERT: L 161 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6795 (tp30) REVERT: M 11 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.5124 (tt) REVERT: N 161 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6790 (tp30) REVERT: N 213 GLU cc_start: 0.3286 (tt0) cc_final: 0.1798 (tm-30) outliers start: 92 outliers final: 46 residues processed: 289 average time/residue: 0.2340 time to fit residues: 106.9566 Evaluate side-chains 241 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Chi-restraints excluded: chain N residue 209 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 254 optimal weight: 20.0000 chunk 414 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 434 optimal weight: 7.9990 chunk 400 optimal weight: 50.0000 chunk 138 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.151082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106709 restraints weight = 131916.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108104 restraints weight = 61278.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108765 restraints weight = 33795.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.109247 restraints weight = 23105.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109284 restraints weight = 21194.199| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 34554 Z= 0.339 Angle : 0.820 12.787 46992 Z= 0.413 Chirality : 0.050 0.336 5370 Planarity : 0.006 0.072 5994 Dihedral : 6.431 44.320 4753 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.93 % Favored : 87.93 % Rotamer: Outliers : 2.74 % Allowed : 9.33 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.12), residues: 4368 helix: -0.46 (0.17), residues: 840 sheet: -2.29 (0.13), residues: 1452 loop : -1.91 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 108 TYR 0.027 0.002 TYR B 254 PHE 0.039 0.002 PHE A 64 TRP 0.053 0.003 TRP K 36 HIS 0.008 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00774 (34530) covalent geometry : angle 0.82005 (46944) SS BOND : bond 0.00331 ( 24) SS BOND : angle 0.54967 ( 48) hydrogen bonds : bond 0.04044 ( 1157) hydrogen bonds : angle 6.47763 ( 3120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 185 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.9009 (tptp) cc_final: 0.8767 (tptp) REVERT: A 97 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8531 (pp) REVERT: A 200 MET cc_start: 0.9093 (mmm) cc_final: 0.8783 (mmm) REVERT: E 108 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7768 (ppp80) REVERT: G 173 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8302 (tm) REVERT: F 97 VAL cc_start: 0.9416 (OUTLIER) cc_final: 0.9029 (t) REVERT: B 97 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8589 (pp) REVERT: B 212 MET cc_start: 0.9178 (mmm) cc_final: 0.8709 (tpt) REVERT: C 97 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8522 (pp) REVERT: C 200 MET cc_start: 0.8995 (mmt) cc_final: 0.8449 (mmt) REVERT: J 95 LEU cc_start: 0.9112 (tp) cc_final: 0.8643 (mp) REVERT: J 197 TYR cc_start: 0.8291 (p90) cc_final: 0.7850 (p90) REVERT: J 198 PHE cc_start: 0.8140 (m-80) cc_final: 0.7884 (m-80) REVERT: J 200 MET cc_start: 0.0648 (mtp) cc_final: 0.0414 (mtp) REVERT: J 265 TYR cc_start: 0.4838 (t80) cc_final: 0.4566 (t80) REVERT: J 279 ASN cc_start: 0.7117 (t0) cc_final: 0.6798 (t0) REVERT: K 29 PHE cc_start: 0.6286 (t80) cc_final: 0.6032 (t80) REVERT: K 81 MET cc_start: 0.4489 (tmm) cc_final: 0.4278 (ptm) REVERT: P 81 MET cc_start: 0.2913 (ttp) cc_final: 0.2701 (ttt) REVERT: P 204 LYS cc_start: 0.7505 (mmmt) cc_final: 0.6871 (tptp) REVERT: P 209 LYS cc_start: 0.5136 (tptt) cc_final: 0.4921 (tppt) REVERT: Q 95 LEU cc_start: 0.8703 (tp) cc_final: 0.8249 (mp) REVERT: Q 172 LYS cc_start: 0.4079 (pttm) cc_final: 0.3730 (mmtm) REVERT: R 24 VAL cc_start: 0.4203 (OUTLIER) cc_final: 0.3881 (p) REVERT: R 95 LEU cc_start: 0.8961 (tp) cc_final: 0.8556 (mp) REVERT: R 197 TYR cc_start: 0.8346 (p90) cc_final: 0.7956 (p90) REVERT: R 288 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: I 34 HIS cc_start: 0.9450 (OUTLIER) cc_final: 0.9169 (m-70) REVERT: I 108 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7860 (ppp80) REVERT: H 108 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7706 (ppp80) REVERT: L 123 GLU cc_start: 0.2822 (tt0) cc_final: 0.2011 (mm-30) REVERT: L 148 TRP cc_start: 0.3750 (m100) cc_final: 0.3297 (m100) REVERT: L 161 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6989 (tp30) REVERT: L 173 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5937 (t80) REVERT: N 161 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6907 (tp30) REVERT: N 213 GLU cc_start: 0.3238 (tt0) cc_final: 0.1784 (tm-30) outliers start: 103 outliers final: 68 residues processed: 271 average time/residue: 0.2278 time to fit residues: 97.2098 Evaluate side-chains 242 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 162 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 295 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 34 HIS Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Chi-restraints excluded: chain N residue 209 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 434 optimal weight: 20.0000 chunk 212 optimal weight: 5.9990 chunk 364 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 302 optimal weight: 30.0000 chunk 145 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 228 optimal weight: 0.0270 chunk 70 optimal weight: 10.0000 chunk 43 optimal weight: 0.0010 overall best weight: 0.5646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN M 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.156269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111906 restraints weight = 128264.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114019 restraints weight = 58073.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114921 restraints weight = 27302.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115044 restraints weight = 19459.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.115169 restraints weight = 19485.306| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 34554 Z= 0.125 Angle : 0.671 10.865 46992 Z= 0.339 Chirality : 0.046 0.173 5370 Planarity : 0.005 0.062 5994 Dihedral : 5.983 41.056 4753 Min Nonbonded Distance : 1.467 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.11 % Favored : 90.82 % Rotamer: Outliers : 2.07 % Allowed : 10.05 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.13), residues: 4368 helix: -0.09 (0.18), residues: 828 sheet: -2.04 (0.13), residues: 1452 loop : -1.73 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 213 TYR 0.036 0.002 TYR Q 254 PHE 0.028 0.002 PHE A 64 TRP 0.056 0.002 TRP O 36 HIS 0.005 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00276 (34530) covalent geometry : angle 0.67129 (46944) SS BOND : bond 0.00199 ( 24) SS BOND : angle 0.55553 ( 48) hydrogen bonds : bond 0.03333 ( 1157) hydrogen bonds : angle 6.02720 ( 3120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 201 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8835 (tptp) cc_final: 0.8611 (tptp) REVERT: A 97 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8197 (pp) REVERT: A 200 MET cc_start: 0.9095 (mmm) cc_final: 0.8531 (mpp) REVERT: E 108 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7564 (ppp80) REVERT: F 34 MET cc_start: 0.8921 (mmm) cc_final: 0.8383 (tpt) REVERT: B 97 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8184 (pp) REVERT: B 212 MET cc_start: 0.9075 (mmm) cc_final: 0.8613 (tpt) REVERT: C 6 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7789 (ptp90) REVERT: C 97 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8254 (pp) REVERT: J 95 LEU cc_start: 0.9076 (tp) cc_final: 0.8639 (mp) REVERT: J 197 TYR cc_start: 0.8210 (p90) cc_final: 0.7739 (p90) REVERT: J 200 MET cc_start: 0.0593 (mtp) cc_final: 0.0336 (mtp) REVERT: J 265 TYR cc_start: 0.4580 (t80) cc_final: 0.4336 (t80) REVERT: J 279 ASN cc_start: 0.7182 (t0) cc_final: 0.6861 (t0) REVERT: J 290 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7760 (m) REVERT: K 29 PHE cc_start: 0.6436 (t80) cc_final: 0.6022 (t80) REVERT: P 81 MET cc_start: 0.3178 (ttp) cc_final: 0.2944 (ttt) REVERT: P 157 TRP cc_start: -0.0139 (m100) cc_final: -0.0762 (m100) REVERT: Q 95 LEU cc_start: 0.8702 (tp) cc_final: 0.8265 (mp) REVERT: Q 122 TRP cc_start: 0.5379 (t-100) cc_final: 0.5065 (t-100) REVERT: Q 172 LYS cc_start: 0.4306 (pttm) cc_final: 0.4008 (mmtm) REVERT: Q 291 ARG cc_start: 0.7725 (ttp-170) cc_final: 0.7368 (tmm-80) REVERT: R 24 VAL cc_start: 0.4368 (OUTLIER) cc_final: 0.4168 (p) REVERT: R 95 LEU cc_start: 0.8931 (tp) cc_final: 0.8500 (mp) REVERT: R 158 ASP cc_start: 0.6080 (p0) cc_final: 0.5819 (t0) REVERT: R 197 TYR cc_start: 0.8235 (p90) cc_final: 0.7844 (p90) REVERT: R 291 ARG cc_start: 0.8199 (ttm170) cc_final: 0.7384 (tmm-80) REVERT: I 108 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7743 (ppp80) REVERT: H 70 ASP cc_start: 0.8636 (p0) cc_final: 0.8425 (p0) REVERT: H 108 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7560 (ppp80) REVERT: L 148 TRP cc_start: 0.3681 (m100) cc_final: 0.3254 (m100) REVERT: L 173 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5892 (t80) REVERT: M 11 LEU cc_start: 0.5425 (OUTLIER) cc_final: 0.5148 (tt) REVERT: N 81 GLU cc_start: 0.6531 (tm-30) cc_final: 0.6310 (tm-30) REVERT: N 161 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6503 (tp30) REVERT: N 213 GLU cc_start: 0.3140 (tt0) cc_final: 0.1582 (tm-30) outliers start: 78 outliers final: 50 residues processed: 260 average time/residue: 0.2200 time to fit residues: 92.3230 Evaluate side-chains 227 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 80 TYR Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 126 HIS Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 379 optimal weight: 30.0000 chunk 130 optimal weight: 0.0070 chunk 141 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 422 optimal weight: 40.0000 chunk 7 optimal weight: 3.9990 chunk 375 optimal weight: 50.0000 chunk 198 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.155416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110710 restraints weight = 129653.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112493 restraints weight = 54763.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113318 restraints weight = 30757.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114018 restraints weight = 18165.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113973 restraints weight = 15651.180| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34554 Z= 0.160 Angle : 0.669 10.974 46992 Z= 0.339 Chirality : 0.046 0.175 5370 Planarity : 0.005 0.062 5994 Dihedral : 5.839 39.884 4753 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.36 % Favored : 90.54 % Rotamer: Outliers : 2.26 % Allowed : 10.58 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.52 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.13), residues: 4368 helix: -0.04 (0.18), residues: 840 sheet: -1.89 (0.13), residues: 1452 loop : -1.71 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 225 TYR 0.028 0.002 TYR Q 254 PHE 0.024 0.002 PHE C 64 TRP 0.062 0.002 TRP O 36 HIS 0.007 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00367 (34530) covalent geometry : angle 0.66927 (46944) SS BOND : bond 0.00290 ( 24) SS BOND : angle 0.56039 ( 48) hydrogen bonds : bond 0.03334 ( 1157) hydrogen bonds : angle 5.84164 ( 3120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 172 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8841 (tptp) cc_final: 0.8635 (tptp) REVERT: A 97 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8333 (pp) REVERT: A 200 MET cc_start: 0.9147 (mmm) cc_final: 0.8490 (mpp) REVERT: E 108 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7490 (ppp80) REVERT: G 173 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8312 (tm) REVERT: B 97 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8341 (pp) REVERT: B 212 MET cc_start: 0.9113 (mmm) cc_final: 0.8596 (tpt) REVERT: C 97 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8338 (pp) REVERT: J 95 LEU cc_start: 0.9100 (tp) cc_final: 0.8653 (mp) REVERT: J 197 TYR cc_start: 0.8294 (p90) cc_final: 0.7776 (p90) REVERT: J 265 TYR cc_start: 0.4519 (t80) cc_final: 0.4290 (t80) REVERT: J 279 ASN cc_start: 0.7003 (t0) cc_final: 0.6662 (t0) REVERT: O 179 TYR cc_start: 0.5284 (m-80) cc_final: 0.4655 (t80) REVERT: Q 95 LEU cc_start: 0.8721 (tp) cc_final: 0.8303 (mp) REVERT: Q 172 LYS cc_start: 0.4666 (pttm) cc_final: 0.4349 (mmtm) REVERT: R 24 VAL cc_start: 0.4350 (OUTLIER) cc_final: 0.4144 (p) REVERT: R 95 LEU cc_start: 0.8920 (tp) cc_final: 0.8521 (mp) REVERT: R 197 TYR cc_start: 0.8309 (p90) cc_final: 0.7932 (p90) REVERT: R 288 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: R 291 ARG cc_start: 0.8096 (ttm170) cc_final: 0.7498 (tmm-80) REVERT: I 4 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8473 (mm) REVERT: I 108 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7533 (ppp80) REVERT: H 70 ASP cc_start: 0.8573 (p0) cc_final: 0.8320 (p0) REVERT: H 108 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7455 (ppp80) REVERT: L 148 TRP cc_start: 0.3745 (m100) cc_final: 0.3281 (m100) REVERT: L 209 PHE cc_start: 0.2529 (p90) cc_final: 0.1511 (m-10) REVERT: M 11 LEU cc_start: 0.5325 (OUTLIER) cc_final: 0.5093 (tt) REVERT: N 148 TRP cc_start: 0.3569 (m100) cc_final: 0.3050 (m100) REVERT: N 161 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6809 (tp30) REVERT: N 213 GLU cc_start: 0.3059 (tt0) cc_final: 0.1853 (tm-30) outliers start: 85 outliers final: 57 residues processed: 242 average time/residue: 0.2121 time to fit residues: 83.0156 Evaluate side-chains 229 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 161 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 80 TYR Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 HIS Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 280 optimal weight: 30.0000 chunk 297 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** 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 = 0.4357 r_free = 0.4357 target = 0.153512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107315 restraints weight = 128788.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108812 restraints weight = 53156.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110054 restraints weight = 30269.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110681 restraints weight = 20644.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111153 restraints weight = 16026.887| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 34554 Z= 0.298 Angle : 0.769 11.653 46992 Z= 0.390 Chirality : 0.048 0.176 5370 Planarity : 0.006 0.233 5994 Dihedral : 6.098 41.528 4753 Min Nonbonded Distance : 1.348 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.38 % Favored : 88.46 % Rotamer: Outliers : 2.31 % Allowed : 10.95 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.14 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.13), residues: 4368 helix: -0.16 (0.17), residues: 840 sheet: -1.88 (0.13), residues: 1452 loop : -1.79 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 38 TYR 0.023 0.002 TYR Q 254 PHE 0.060 0.002 PHE R 240 TRP 0.075 0.003 TRP O 36 HIS 0.008 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00684 (34530) covalent geometry : angle 0.76943 (46944) SS BOND : bond 0.00313 ( 24) SS BOND : angle 0.60403 ( 48) hydrogen bonds : bond 0.03775 ( 1157) hydrogen bonds : angle 6.03244 ( 3120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 167 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8905 (tptp) cc_final: 0.8701 (tptp) REVERT: A 97 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8449 (pp) REVERT: A 200 MET cc_start: 0.9116 (mmm) cc_final: 0.8365 (mpp) REVERT: E 108 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7518 (ppp80) REVERT: G 173 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8323 (tm) REVERT: F 97 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8889 (t) REVERT: B 97 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8543 (pp) REVERT: B 212 MET cc_start: 0.9162 (mmm) cc_final: 0.8663 (tpt) REVERT: C 97 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8459 (pp) REVERT: J 95 LEU cc_start: 0.9061 (tp) cc_final: 0.8635 (mp) REVERT: J 176 TYR cc_start: 0.7830 (m-80) cc_final: 0.7128 (m-10) REVERT: J 197 TYR cc_start: 0.8339 (p90) cc_final: 0.7707 (p90) REVERT: J 200 MET cc_start: 0.0662 (mtp) cc_final: 0.0448 (mtp) REVERT: J 265 TYR cc_start: 0.4464 (t80) cc_final: 0.4217 (t80) REVERT: J 279 ASN cc_start: 0.6914 (t0) cc_final: 0.6563 (t0) REVERT: K 38 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7597 (tmm-80) REVERT: O 179 TYR cc_start: 0.5252 (m-80) cc_final: 0.4717 (t80) REVERT: P 157 TRP cc_start: 0.0005 (m100) cc_final: -0.0812 (m100) REVERT: Q 95 LEU cc_start: 0.8670 (tp) cc_final: 0.8241 (mp) REVERT: Q 172 LYS cc_start: 0.4747 (pttm) cc_final: 0.4409 (mmtm) REVERT: R 24 VAL cc_start: 0.4324 (OUTLIER) cc_final: 0.4084 (p) REVERT: R 95 LEU cc_start: 0.8877 (tp) cc_final: 0.8470 (mp) REVERT: R 197 TYR cc_start: 0.8453 (p90) cc_final: 0.8240 (p90) REVERT: R 288 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: R 290 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7888 (m) REVERT: I 4 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8581 (mm) REVERT: I 34 HIS cc_start: 0.9435 (OUTLIER) cc_final: 0.9152 (m-70) REVERT: I 108 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7661 (ppp80) REVERT: H 108 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7542 (ppp80) REVERT: L 148 TRP cc_start: 0.3729 (m100) cc_final: 0.3424 (m100) REVERT: L 173 TYR cc_start: 0.6525 (t80) cc_final: 0.6305 (t80) REVERT: L 192 TYR cc_start: 0.4461 (m-10) cc_final: 0.3868 (m-10) REVERT: L 209 PHE cc_start: 0.2736 (p90) cc_final: 0.1592 (m-10) REVERT: M 11 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4860 (tt) REVERT: N 161 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6805 (tp30) REVERT: N 213 GLU cc_start: 0.2971 (tt0) cc_final: 0.1607 (tm-30) outliers start: 87 outliers final: 62 residues processed: 239 average time/residue: 0.2149 time to fit residues: 82.9729 Evaluate side-chains 233 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 156 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 35 ASN Chi-restraints excluded: chain O residue 36 TRP Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 80 TYR Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 126 HIS Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain R residue 290 THR Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 HIS Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 117 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 202 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 138 optimal weight: 0.1980 chunk 113 optimal weight: 7.9990 chunk 336 optimal weight: 0.9980 chunk 356 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN ** H 189 HIS ** 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 = 0.4404 r_free = 0.4404 target = 0.156014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111731 restraints weight = 126374.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114082 restraints weight = 51997.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.114719 restraints weight = 28698.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115392 restraints weight = 18376.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.115605 restraints weight = 15390.447| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34554 Z= 0.126 Angle : 0.674 10.801 46992 Z= 0.342 Chirality : 0.046 0.173 5370 Planarity : 0.005 0.057 5994 Dihedral : 5.730 38.926 4753 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.97 % Favored : 90.96 % Rotamer: Outliers : 2.07 % Allowed : 11.19 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.14 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.13), residues: 4368 helix: 0.18 (0.18), residues: 828 sheet: -1.72 (0.13), residues: 1452 loop : -1.58 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 38 TYR 0.037 0.002 TYR R 254 PHE 0.033 0.002 PHE J 240 TRP 0.066 0.002 TRP O 36 HIS 0.008 0.001 HIS Q 101 Details of bonding type rmsd covalent geometry : bond 0.00280 (34530) covalent geometry : angle 0.67385 (46944) SS BOND : bond 0.00256 ( 24) SS BOND : angle 0.51857 ( 48) hydrogen bonds : bond 0.03230 ( 1157) hydrogen bonds : angle 5.65242 ( 3120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 177 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8193 (pp) REVERT: A 200 MET cc_start: 0.9072 (mmm) cc_final: 0.8513 (mpp) REVERT: D 37 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8667 (m) REVERT: E 108 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7380 (ppp80) REVERT: E 175 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9061 (mm) REVERT: B 6 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7370 (pmt170) REVERT: B 97 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8186 (pp) REVERT: B 212 MET cc_start: 0.9082 (mmm) cc_final: 0.8571 (tpt) REVERT: C 6 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7735 (ptp90) REVERT: C 97 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8209 (pp) REVERT: J 95 LEU cc_start: 0.9115 (tp) cc_final: 0.8716 (mt) REVERT: J 176 TYR cc_start: 0.7590 (m-80) cc_final: 0.6884 (m-10) REVERT: J 197 TYR cc_start: 0.8227 (p90) cc_final: 0.7585 (p90) REVERT: J 200 MET cc_start: 0.0866 (mtp) cc_final: 0.0613 (mtp) REVERT: J 212 MET cc_start: 0.1902 (mmp) cc_final: 0.1172 (mmp) REVERT: J 259 TYR cc_start: 0.8032 (t80) cc_final: 0.7541 (t80) REVERT: J 279 ASN cc_start: 0.6958 (t0) cc_final: 0.6609 (t0) REVERT: J 291 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7193 (tmm-80) REVERT: K 38 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7489 (tmm-80) REVERT: Q 95 LEU cc_start: 0.8760 (tp) cc_final: 0.8340 (mp) REVERT: Q 172 LYS cc_start: 0.4821 (pttm) cc_final: 0.4521 (mmtm) REVERT: R 24 VAL cc_start: 0.4581 (OUTLIER) cc_final: 0.4317 (p) REVERT: R 95 LEU cc_start: 0.8842 (tp) cc_final: 0.8417 (mp) REVERT: R 176 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.5904 (m-80) REVERT: R 197 TYR cc_start: 0.8320 (p90) cc_final: 0.7528 (p90) REVERT: R 288 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: R 291 ARG cc_start: 0.8423 (ttm170) cc_final: 0.7854 (tmm-80) REVERT: I 108 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7487 (ppp80) REVERT: H 108 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7333 (ppp80) REVERT: L 148 TRP cc_start: 0.3591 (m100) cc_final: 0.3192 (m100) REVERT: L 209 PHE cc_start: 0.2344 (p90) cc_final: 0.1296 (m-10) REVERT: M 11 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.5159 (tt) REVERT: N 148 TRP cc_start: 0.3634 (m100) cc_final: 0.3105 (m100) REVERT: N 161 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6515 (tp30) REVERT: N 213 GLU cc_start: 0.3248 (tt0) cc_final: 0.1797 (tm-30) outliers start: 78 outliers final: 50 residues processed: 237 average time/residue: 0.2186 time to fit residues: 83.8788 Evaluate side-chains 227 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 35 ASN Chi-restraints excluded: chain O residue 36 TRP Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 80 TYR Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 126 HIS Chi-restraints excluded: chain Q residue 176 TYR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 176 TYR Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 HIS Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 317 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 427 optimal weight: 30.0000 chunk 78 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 303 optimal weight: 40.0000 chunk 306 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** 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 = 0.4385 r_free = 0.4385 target = 0.154876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111846 restraints weight = 127174.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112744 restraints weight = 59181.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113959 restraints weight = 34864.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114042 restraints weight = 21177.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114205 restraints weight = 20441.986| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 34554 Z= 0.187 Angle : 0.689 10.858 46992 Z= 0.349 Chirality : 0.046 0.181 5370 Planarity : 0.005 0.058 5994 Dihedral : 5.721 38.885 4753 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.55 % Favored : 90.38 % Rotamer: Outliers : 1.99 % Allowed : 11.30 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.13), residues: 4368 helix: 0.12 (0.18), residues: 840 sheet: -1.67 (0.13), residues: 1452 loop : -1.62 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 45 TYR 0.034 0.002 TYR R 254 PHE 0.042 0.002 PHE A 64 TRP 0.064 0.002 TRP O 36 HIS 0.005 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00431 (34530) covalent geometry : angle 0.68888 (46944) SS BOND : bond 0.00285 ( 24) SS BOND : angle 0.57013 ( 48) hydrogen bonds : bond 0.03318 ( 1157) hydrogen bonds : angle 5.61986 ( 3120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 163 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8464 (pp) REVERT: A 200 MET cc_start: 0.9186 (mmm) cc_final: 0.8538 (mpp) REVERT: E 108 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7329 (ppp80) REVERT: E 175 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9063 (mm) REVERT: B 97 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8483 (pp) REVERT: B 212 MET cc_start: 0.9103 (mmm) cc_final: 0.8608 (tpt) REVERT: C 97 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8471 (pp) REVERT: J 95 LEU cc_start: 0.9108 (tp) cc_final: 0.8699 (mt) REVERT: J 176 TYR cc_start: 0.7569 (m-80) cc_final: 0.6852 (m-10) REVERT: J 197 TYR cc_start: 0.8219 (p90) cc_final: 0.7569 (p90) REVERT: J 200 MET cc_start: 0.0909 (mtp) cc_final: 0.0639 (mtp) REVERT: J 279 ASN cc_start: 0.7026 (t0) cc_final: 0.6678 (t0) REVERT: K 38 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7506 (tmm-80) REVERT: Q 95 LEU cc_start: 0.8808 (tp) cc_final: 0.8406 (mt) REVERT: Q 172 LYS cc_start: 0.4891 (pttm) cc_final: 0.4581 (mmtm) REVERT: R 24 VAL cc_start: 0.4632 (OUTLIER) cc_final: 0.4381 (p) REVERT: R 95 LEU cc_start: 0.8877 (tp) cc_final: 0.8458 (mp) REVERT: R 197 TYR cc_start: 0.8440 (p90) cc_final: 0.7990 (p90) REVERT: R 288 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: I 78 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.5535 (mt) REVERT: I 108 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7462 (ppp80) REVERT: H 108 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7417 (ppp80) REVERT: L 148 TRP cc_start: 0.3517 (m100) cc_final: 0.3191 (m100) REVERT: L 192 TYR cc_start: 0.4423 (m-10) cc_final: 0.3895 (m-10) REVERT: L 209 PHE cc_start: 0.2168 (p90) cc_final: 0.1191 (m-10) REVERT: M 11 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.4954 (tt) REVERT: M 94 TRP cc_start: 0.6985 (m100) cc_final: 0.6522 (m100) REVERT: N 148 TRP cc_start: 0.3552 (m100) cc_final: 0.3136 (m100) REVERT: N 161 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6437 (tp30) REVERT: N 213 GLU cc_start: 0.3172 (tt0) cc_final: 0.1705 (tm-30) outliers start: 75 outliers final: 59 residues processed: 226 average time/residue: 0.2237 time to fit residues: 81.4026 Evaluate side-chains 227 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 156 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 35 ASN Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 80 TYR Chi-restraints excluded: chain O residue 98 TYR Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 126 HIS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 HIS Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 231 optimal weight: 50.0000 chunk 70 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 242 optimal weight: 50.0000 chunk 135 optimal weight: 0.7980 chunk 220 optimal weight: 20.0000 chunk 46 optimal weight: 0.4980 chunk 358 optimal weight: 0.6980 chunk 407 optimal weight: 40.0000 chunk 295 optimal weight: 0.7980 chunk 276 optimal weight: 30.0000 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.159917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.121659 restraints weight = 137717.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.120401 restraints weight = 76158.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.121630 restraints weight = 49532.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121476 restraints weight = 41217.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.121749 restraints weight = 32122.450| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34554 Z= 0.154 Angle : 0.675 11.494 46992 Z= 0.342 Chirality : 0.046 0.210 5370 Planarity : 0.005 0.057 5994 Dihedral : 5.644 38.286 4753 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.09 % Favored : 90.87 % Rotamer: Outliers : 1.97 % Allowed : 11.35 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.13), residues: 4368 helix: 0.16 (0.18), residues: 840 sheet: -1.60 (0.13), residues: 1452 loop : -1.62 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 291 TYR 0.037 0.002 TYR R 254 PHE 0.038 0.002 PHE A 64 TRP 0.056 0.002 TRP K 36 HIS 0.005 0.001 HIS R 141 Details of bonding type rmsd covalent geometry : bond 0.00353 (34530) covalent geometry : angle 0.67506 (46944) SS BOND : bond 0.00269 ( 24) SS BOND : angle 0.55079 ( 48) hydrogen bonds : bond 0.03235 ( 1157) hydrogen bonds : angle 5.53909 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6599.37 seconds wall clock time: 115 minutes 21.38 seconds (6921.38 seconds total)