Starting phenix.real_space_refine on Fri Sep 27 11:18:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/09_2024/8en7_28269.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/09_2024/8en7_28269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/09_2024/8en7_28269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/09_2024/8en7_28269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/09_2024/8en7_28269.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/09_2024/8en7_28269.cif" } resolution = 1.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 35064 atoms to isotropic. 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 Fe 6 7.16 5 S 192 5.16 5 C 21960 2.51 5 N 6168 2.21 5 O 9288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 37614 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "B" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "C" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "D" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "E" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "F" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "G" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "H" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "I" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "J" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "K" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "L" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "M" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "N" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "O" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "P" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "Q" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "R" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "S" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "T" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "U" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "V" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "W" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "X" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1381 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "G" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "H" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "I" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "J" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "L" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "M" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "N" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "O" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "P" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "Q" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "S" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "U" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "V" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "W" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "X" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Residues with excluded nonbonded symmetry interactions: 150 residue: pdb=" N AARG A 63 " occ=0.47 ... (20 atoms not shown) pdb=" NH2BARG A 63 " occ=0.53 residue: pdb=" N AGLU A 64 " occ=0.47 ... (16 atoms not shown) pdb=" OE2BGLU A 64 " occ=0.53 residue: pdb=" N AGLU A 94 " occ=0.59 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.41 residue: pdb=" N AILE A 133 " occ=0.60 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.40 residue: pdb=" N ASER A 144 " occ=0.56 ... (10 atoms not shown) pdb=" OG BSER A 144 " occ=0.45 residue: pdb=" N ALYS A 172 " occ=0.55 ... (16 atoms not shown) pdb=" NZ BLYS A 172 " occ=0.45 residue: pdb=" N AARG B 63 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG B 63 " occ=0.52 residue: pdb=" N AGLU B 64 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 64 " occ=0.52 residue: pdb=" N AGLU B 94 " occ=0.59 ... (16 atoms not shown) pdb=" OE2BGLU B 94 " occ=0.41 residue: pdb=" N AILE B 133 " occ=0.59 ... (14 atoms not shown) pdb=" CD1BILE B 133 " occ=0.41 residue: pdb=" N ASER B 144 " occ=0.56 ... (10 atoms not shown) pdb=" OG BSER B 144 " occ=0.44 residue: pdb=" N ALYS B 172 " occ=0.55 ... (16 atoms not shown) pdb=" NZ BLYS B 172 " occ=0.45 ... (remaining 138 not shown) Time building chain proxies: 27.78, per 1000 atoms: 0.74 Number of scatterers: 37614 At special positions: 0 Unit cell: (132.379, 132.379, 132.379, 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) Fe 6 26.01 S 192 16.00 O 9288 8.00 N 6168 7.00 C 21960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.76 Conformation dependent library (CDL) restraints added in 6.2 seconds 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 13 through 41 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 41 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 164 through 174 removed outlier: 4.248A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 41 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 41 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 41 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 41 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 41 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 41 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 41 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 41 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 41 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 41 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 41 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 41 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 41 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 41 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 41 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 41 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 41 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 41 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 41 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 41 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 41 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 41 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2832 hydrogen bonds defined for protein. 8592 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: 10.63 Time building geometry restraints manager: 9.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8612 1.33 - 1.45: 8980 1.45 - 1.58: 17976 1.58 - 1.71: 0 1.71 - 1.83: 312 Bond restraints: 35880 Sorted by residual: bond pdb=" C BGLU G 64 " pdb=" N HIS G 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 bond pdb=" C BGLU F 64 " pdb=" N HIS F 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 bond pdb=" C BGLU X 64 " pdb=" N HIS X 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 bond pdb=" C BGLU L 64 " pdb=" N HIS L 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 bond pdb=" C BGLU V 64 " pdb=" N HIS V 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 ... (remaining 35875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 46292 2.77 - 5.54: 1898 5.54 - 8.31: 145 8.31 - 11.08: 72 11.08 - 13.85: 1 Bond angle restraints: 48408 Sorted by residual: angle pdb=" CB GLU X 167 " pdb=" CG GLU X 167 " pdb=" CD GLU X 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" CB GLU W 167 " pdb=" CG GLU W 167 " pdb=" CD GLU W 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" CB GLU I 167 " pdb=" CG GLU I 167 " pdb=" CD GLU I 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" CB GLU U 167 " pdb=" CG GLU U 167 " pdb=" CD GLU U 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" CB GLU P 167 " pdb=" CG GLU P 167 " pdb=" CD GLU P 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 ... (remaining 48403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 21527 35.99 - 71.97: 361 71.97 - 107.96: 72 107.96 - 143.94: 0 143.94 - 179.93: 24 Dihedral angle restraints: 21984 sinusoidal: 9192 harmonic: 12792 Sorted by residual: dihedral pdb=" CD BARG A 63 " pdb=" NE BARG A 63 " pdb=" CZ BARG A 63 " pdb=" NH1BARG A 63 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG B 63 " pdb=" NE BARG B 63 " pdb=" CZ BARG B 63 " pdb=" NH1BARG B 63 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG D 63 " pdb=" NE BARG D 63 " pdb=" CZ BARG D 63 " pdb=" NH1BARG D 63 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 21981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3361 0.068 - 0.135: 1414 0.135 - 0.203: 144 0.203 - 0.270: 73 0.270 - 0.338: 24 Chirality restraints: 5016 Sorted by residual: chirality pdb=" CB VAL C 8 " pdb=" CA VAL C 8 " pdb=" CG1 VAL C 8 " pdb=" CG2 VAL C 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB VAL O 8 " pdb=" CA VAL O 8 " pdb=" CG1 VAL O 8 " pdb=" CG2 VAL O 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL D 8 " pdb=" CA VAL D 8 " pdb=" CG1 VAL D 8 " pdb=" CG2 VAL D 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 5013 not shown) Planarity restraints: 6432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 137 " 0.092 2.00e-02 2.50e+03 4.94e-02 4.88e+01 pdb=" CG TYR C 137 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 137 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR C 137 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR C 137 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 137 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR C 137 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 137 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 137 " -0.092 2.00e-02 2.50e+03 4.93e-02 4.86e+01 pdb=" CG TYR D 137 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR D 137 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR D 137 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR D 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR D 137 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR D 137 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 137 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 137 " -0.092 2.00e-02 2.50e+03 4.93e-02 4.86e+01 pdb=" CG TYR S 137 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR S 137 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR S 137 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR S 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR S 137 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR S 137 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR S 137 " -0.065 2.00e-02 2.50e+03 ... (remaining 6429 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.57: 95 1.57 - 2.40: 376 2.40 - 3.23: 42158 3.23 - 4.07: 123097 4.07 - 4.90: 210013 Warning: very small nonbonded interaction distances. Nonbonded interactions: 375739 Sorted by model distance: nonbonded pdb=" NH2AARG C 63 " pdb=" NH2AARG E 63 " model vdw 0.731 3.200 nonbonded pdb=" NH2AARG G 63 " pdb=" NH2AARG U 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2AARG A 63 " pdb=" NH2AARG K 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2AARG D 63 " pdb=" NH2AARG Q 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2AARG F 63 " pdb=" NH2AARG N 63 " model vdw 0.733 3.200 ... (remaining 375734 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'B' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'C' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'D' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'E' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'F' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'G' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'H' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'I' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'J' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'K' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'L' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'M' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'N' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'O' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'P' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'Q' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'R' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'S' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'T' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'U' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'V' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'W' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'X' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) } 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=0.16 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.360 Construct map_model_manager: 0.040 Extract box with map and model: 1.410 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 80.900 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.200 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.012 0.227 35880 Z= 0.779 Angle : 1.294 13.854 48408 Z= 0.863 Chirality : 0.072 0.338 5016 Planarity : 0.009 0.049 6432 Dihedral : 15.669 179.927 13776 Min Nonbonded Distance : 0.731 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 5.09 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.12), residues: 4464 helix: 1.92 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.57 (0.22), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.009 TRP H 93 HIS 0.013 0.003 HIS L 60 PHE 0.028 0.007 PHE V 51 TYR 0.092 0.013 TYR C 137 ARG 0.015 0.002 ARG T 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 866 time to evaluate : 3.249 Fit side-chains REVERT: A 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7289 (mppt) REVERT: A 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: A 68 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7327 (tttm) REVERT: A 75 GLN cc_start: 0.7707 (mt0) cc_final: 0.7488 (tt0) REVERT: A 139 SER cc_start: 0.7859 (m) cc_final: 0.7658 (t) REVERT: A 143 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7521 (mttt) REVERT: B 49 LYS cc_start: 0.7729 (mttm) cc_final: 0.7289 (mppt) REVERT: B 53 LYS cc_start: 0.7530 (ttpp) cc_final: 0.7161 (ttpp) REVERT: B 68 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7322 (tttm) REVERT: B 75 GLN cc_start: 0.7707 (mt0) cc_final: 0.7486 (tt0) REVERT: B 139 SER cc_start: 0.7859 (m) cc_final: 0.7654 (t) REVERT: B 143 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7510 (mttt) REVERT: C 14 GLN cc_start: 0.7360 (mm-40) cc_final: 0.6975 (mt0) REVERT: C 49 LYS cc_start: 0.7714 (mttm) cc_final: 0.7283 (mppt) REVERT: C 53 LYS cc_start: 0.7487 (ttpp) cc_final: 0.7112 (ttpp) REVERT: C 68 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7353 (tttm) REVERT: C 75 GLN cc_start: 0.7756 (mt0) cc_final: 0.7545 (tt0) REVERT: C 143 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7580 (mttp) REVERT: D 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7292 (mppt) REVERT: D 53 LYS cc_start: 0.7530 (ttpp) cc_final: 0.7158 (ttpp) REVERT: D 68 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7330 (tttm) REVERT: D 75 GLN cc_start: 0.7703 (mt0) cc_final: 0.7488 (tt0) REVERT: D 139 SER cc_start: 0.7860 (m) cc_final: 0.7658 (t) REVERT: D 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7520 (mttt) REVERT: E 49 LYS cc_start: 0.7731 (mttm) cc_final: 0.7294 (mppt) REVERT: E 53 LYS cc_start: 0.7532 (ttpp) cc_final: 0.7161 (ttpp) REVERT: E 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7327 (tttm) REVERT: E 75 GLN cc_start: 0.7702 (mt0) cc_final: 0.7486 (tt0) REVERT: E 139 SER cc_start: 0.7860 (m) cc_final: 0.7660 (t) REVERT: E 143 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7520 (mttt) REVERT: F 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7291 (mppt) REVERT: F 53 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7158 (ttpp) REVERT: F 68 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: F 75 GLN cc_start: 0.7701 (mt0) cc_final: 0.7486 (tt0) REVERT: F 139 SER cc_start: 0.7863 (m) cc_final: 0.7660 (t) REVERT: F 143 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7520 (mttt) REVERT: G 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7291 (mppt) REVERT: G 53 LYS cc_start: 0.7527 (ttpp) cc_final: 0.7157 (ttpp) REVERT: G 68 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7326 (tttm) REVERT: G 75 GLN cc_start: 0.7703 (mt0) cc_final: 0.7488 (tt0) REVERT: G 139 SER cc_start: 0.7862 (m) cc_final: 0.7659 (t) REVERT: G 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7520 (mttt) REVERT: H 49 LYS cc_start: 0.7730 (mttm) cc_final: 0.7293 (mppt) REVERT: H 53 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7161 (ttpp) REVERT: H 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7326 (tttm) REVERT: H 75 GLN cc_start: 0.7705 (mt0) cc_final: 0.7485 (tt0) REVERT: H 139 SER cc_start: 0.7859 (m) cc_final: 0.7658 (t) REVERT: H 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7518 (mttt) REVERT: I 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7288 (mppt) REVERT: I 53 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7155 (ttpp) REVERT: I 68 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7323 (tttm) REVERT: I 75 GLN cc_start: 0.7706 (mt0) cc_final: 0.7485 (tt0) REVERT: I 139 SER cc_start: 0.7864 (m) cc_final: 0.7662 (t) REVERT: I 143 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7520 (mttt) REVERT: J 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7289 (mppt) REVERT: J 53 LYS cc_start: 0.7527 (ttpp) cc_final: 0.7157 (ttpp) REVERT: J 68 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7327 (tttm) REVERT: J 75 GLN cc_start: 0.7707 (mt0) cc_final: 0.7489 (tt0) REVERT: J 139 SER cc_start: 0.7862 (m) cc_final: 0.7659 (t) REVERT: J 143 LYS cc_start: 0.7841 (ttmm) cc_final: 0.7519 (mttt) REVERT: K 49 LYS cc_start: 0.7730 (mttm) cc_final: 0.7291 (mppt) REVERT: K 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7158 (ttpp) REVERT: K 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7325 (tttm) REVERT: K 75 GLN cc_start: 0.7707 (mt0) cc_final: 0.7485 (tt0) REVERT: K 139 SER cc_start: 0.7864 (m) cc_final: 0.7662 (t) REVERT: K 143 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7519 (mttt) REVERT: L 49 LYS cc_start: 0.7729 (mttm) cc_final: 0.7290 (mppt) REVERT: L 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: L 68 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: L 75 GLN cc_start: 0.7706 (mt0) cc_final: 0.7488 (tt0) REVERT: L 139 SER cc_start: 0.7862 (m) cc_final: 0.7660 (t) REVERT: L 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7521 (mttt) REVERT: M 49 LYS cc_start: 0.7725 (mttm) cc_final: 0.7291 (mppt) REVERT: M 53 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7157 (ttpp) REVERT: M 68 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7327 (tttm) REVERT: M 75 GLN cc_start: 0.7702 (mt0) cc_final: 0.7487 (tt0) REVERT: M 139 SER cc_start: 0.7859 (m) cc_final: 0.7657 (t) REVERT: M 143 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7520 (mttt) REVERT: N 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7293 (mppt) REVERT: N 53 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7161 (ttpp) REVERT: N 68 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7326 (tttm) REVERT: N 75 GLN cc_start: 0.7701 (mt0) cc_final: 0.7485 (tt0) REVERT: N 139 SER cc_start: 0.7860 (m) cc_final: 0.7659 (t) REVERT: N 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7520 (mttt) REVERT: O 49 LYS cc_start: 0.7731 (mttm) cc_final: 0.7292 (mppt) REVERT: O 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: O 68 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7324 (tttm) REVERT: O 75 GLN cc_start: 0.7704 (mt0) cc_final: 0.7482 (tt0) REVERT: O 139 SER cc_start: 0.7860 (m) cc_final: 0.7660 (t) REVERT: O 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7519 (mttt) REVERT: P 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7289 (mppt) REVERT: P 53 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7157 (ttpp) REVERT: P 68 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7324 (tttm) REVERT: P 75 GLN cc_start: 0.7706 (mt0) cc_final: 0.7483 (tt0) REVERT: P 139 SER cc_start: 0.7859 (m) cc_final: 0.7658 (t) REVERT: P 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7519 (mttt) REVERT: Q 49 LYS cc_start: 0.7732 (mttm) cc_final: 0.7293 (mppt) REVERT: Q 53 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7161 (ttpp) REVERT: Q 68 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7323 (tttm) REVERT: Q 75 GLN cc_start: 0.7705 (mt0) cc_final: 0.7483 (tt0) REVERT: Q 139 SER cc_start: 0.7861 (m) cc_final: 0.7660 (t) REVERT: Q 143 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7520 (mttt) REVERT: R 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7291 (mppt) REVERT: R 53 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7156 (ttpp) REVERT: R 68 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: R 75 GLN cc_start: 0.7700 (mt0) cc_final: 0.7482 (tt0) REVERT: R 139 SER cc_start: 0.7861 (m) cc_final: 0.7660 (t) REVERT: R 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7519 (mttt) REVERT: S 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7291 (mppt) REVERT: S 53 LYS cc_start: 0.7527 (ttpp) cc_final: 0.7158 (ttpp) REVERT: S 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7325 (tttm) REVERT: S 75 GLN cc_start: 0.7703 (mt0) cc_final: 0.7486 (tt0) REVERT: S 139 SER cc_start: 0.7863 (m) cc_final: 0.7661 (t) REVERT: S 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7519 (mttt) REVERT: T 49 LYS cc_start: 0.7729 (mttm) cc_final: 0.7293 (mppt) REVERT: T 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: T 68 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7324 (tttm) REVERT: T 75 GLN cc_start: 0.7701 (mt0) cc_final: 0.7483 (tt0) REVERT: T 139 SER cc_start: 0.7862 (m) cc_final: 0.7661 (t) REVERT: T 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7520 (mttt) REVERT: U 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7292 (mppt) REVERT: U 53 LYS cc_start: 0.7527 (ttpp) cc_final: 0.7157 (ttpp) REVERT: U 68 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7324 (tttm) REVERT: U 75 GLN cc_start: 0.7698 (mt0) cc_final: 0.7479 (tt0) REVERT: U 139 SER cc_start: 0.7861 (m) cc_final: 0.7661 (t) REVERT: U 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7519 (mttt) REVERT: V 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7292 (mppt) REVERT: V 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: V 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7326 (tttm) REVERT: V 75 GLN cc_start: 0.7702 (mt0) cc_final: 0.7483 (tt0) REVERT: V 143 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7518 (mttt) REVERT: W 49 LYS cc_start: 0.7729 (mttm) cc_final: 0.7291 (mppt) REVERT: W 53 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7157 (ttpp) REVERT: W 68 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7323 (tttm) REVERT: W 75 GLN cc_start: 0.7706 (mt0) cc_final: 0.7485 (tt0) REVERT: W 139 SER cc_start: 0.7861 (m) cc_final: 0.7659 (t) REVERT: W 143 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7518 (mttt) REVERT: X 49 LYS cc_start: 0.7731 (mttm) cc_final: 0.7294 (mppt) REVERT: X 53 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7159 (ttpp) REVERT: X 68 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: X 75 GLN cc_start: 0.7700 (mt0) cc_final: 0.7486 (tt0) REVERT: X 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7519 (mttt) outliers start: 48 outliers final: 0 residues processed: 866 average time/residue: 1.7674 time to fit residues: 1753.7757 Evaluate side-chains 760 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 736 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.6980 chunk 309 optimal weight: 0.6980 chunk 171 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 370 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN A 105 HIS B 60 HIS B 83 GLN B 105 HIS B 173 HIS C 60 HIS C 83 GLN C 105 HIS D 60 HIS D 83 GLN D 105 HIS E 60 HIS E 83 GLN E 105 HIS F 60 HIS F 83 GLN G 60 HIS G 83 GLN H 60 HIS H 83 GLN H 105 HIS I 60 HIS I 83 GLN I 105 HIS J 60 HIS J 83 GLN J 105 HIS K 60 HIS K 83 GLN L 60 HIS L 83 GLN M 60 HIS M 83 GLN M 105 HIS N 60 HIS N 83 GLN N 105 HIS O 60 HIS O 83 GLN O 105 HIS P 60 HIS P 83 GLN P 105 HIS Q 60 HIS Q 83 GLN Q 105 HIS R 60 HIS R 83 GLN R 105 HIS S 60 HIS S 83 GLN S 105 HIS T 60 HIS T 83 GLN T 105 HIS U 60 HIS U 83 GLN U 105 HIS V 60 HIS V 83 GLN V 105 HIS W 60 HIS W 83 GLN X 60 HIS X 83 GLN X 105 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 35880 Z= 0.159 Angle : 0.568 5.821 48408 Z= 0.314 Chirality : 0.037 0.124 5016 Planarity : 0.003 0.024 6432 Dihedral : 13.305 178.766 4896 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 7.04 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.87 (0.13), residues: 4464 helix: 3.70 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 1.06 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 93 HIS 0.004 0.001 HIS C 105 PHE 0.013 0.002 PHE C 41 TYR 0.020 0.002 TYR N 32 ARG 0.002 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 776 time to evaluate : 3.289 Fit side-chains REVERT: A 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7274 (ttpp) REVERT: A 68 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: A 139 SER cc_start: 0.7903 (m) cc_final: 0.7664 (t) REVERT: A 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7644 (mttp) REVERT: B 53 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7273 (ttpp) REVERT: B 68 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7481 (tttm) REVERT: B 139 SER cc_start: 0.7904 (m) cc_final: 0.7665 (t) REVERT: B 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7641 (mttp) REVERT: C 53 LYS cc_start: 0.7693 (ttpp) cc_final: 0.7323 (ttpp) REVERT: C 68 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7483 (tttm) REVERT: C 143 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7654 (mttm) REVERT: D 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7274 (ttpp) REVERT: D 68 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: D 139 SER cc_start: 0.7904 (m) cc_final: 0.7665 (t) REVERT: D 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7642 (mttp) REVERT: E 53 LYS cc_start: 0.7686 (ttpp) cc_final: 0.7273 (ttpp) REVERT: E 68 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7481 (tttm) REVERT: E 139 SER cc_start: 0.7903 (m) cc_final: 0.7664 (t) REVERT: E 143 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7643 (mttp) REVERT: F 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7273 (ttpp) REVERT: F 68 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7464 (tttm) REVERT: F 139 SER cc_start: 0.7902 (m) cc_final: 0.7663 (t) REVERT: F 143 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7645 (mttp) REVERT: G 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7273 (ttpp) REVERT: G 68 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7461 (tttm) REVERT: G 139 SER cc_start: 0.7903 (m) cc_final: 0.7664 (t) REVERT: G 143 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7641 (mttp) REVERT: H 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7275 (ttpp) REVERT: H 68 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: H 139 SER cc_start: 0.7904 (m) cc_final: 0.7665 (t) REVERT: H 143 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7642 (mttp) REVERT: I 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7274 (ttpp) REVERT: I 68 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7464 (tttm) REVERT: I 139 SER cc_start: 0.7903 (m) cc_final: 0.7664 (t) REVERT: I 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7642 (mttp) REVERT: J 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7275 (ttpp) REVERT: J 68 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: J 139 SER cc_start: 0.7904 (m) cc_final: 0.7665 (t) REVERT: J 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7642 (mttp) REVERT: K 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7275 (ttpp) REVERT: K 68 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: K 139 SER cc_start: 0.7904 (m) cc_final: 0.7665 (t) REVERT: K 143 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7645 (mttp) REVERT: L 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7274 (ttpp) REVERT: L 68 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: L 139 SER cc_start: 0.7903 (m) cc_final: 0.7664 (t) REVERT: L 143 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7647 (mttp) REVERT: M 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7273 (ttpp) REVERT: M 68 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: M 139 SER cc_start: 0.7902 (m) cc_final: 0.7664 (t) REVERT: M 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7641 (mttp) REVERT: N 53 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7272 (ttpp) REVERT: N 68 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: N 139 SER cc_start: 0.7902 (m) cc_final: 0.7664 (t) REVERT: N 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7641 (mttp) REVERT: O 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7274 (ttpp) REVERT: O 68 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: O 139 SER cc_start: 0.7903 (m) cc_final: 0.7664 (t) REVERT: O 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7643 (mttp) REVERT: P 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7274 (ttpp) REVERT: P 68 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: P 139 SER cc_start: 0.7902 (m) cc_final: 0.7664 (t) REVERT: P 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7642 (mttp) REVERT: Q 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7273 (ttpp) REVERT: Q 68 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: Q 139 SER cc_start: 0.7903 (m) cc_final: 0.7664 (t) REVERT: Q 143 LYS cc_start: 0.7942 (ttmm) cc_final: 0.7646 (mttp) REVERT: R 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7274 (ttpp) REVERT: R 68 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: R 139 SER cc_start: 0.7904 (m) cc_final: 0.7664 (t) REVERT: R 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7643 (mttp) REVERT: S 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7273 (ttpp) REVERT: S 68 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: S 139 SER cc_start: 0.7903 (m) cc_final: 0.7665 (t) REVERT: S 143 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7643 (mttp) REVERT: T 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7273 (ttpp) REVERT: T 68 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: T 139 SER cc_start: 0.7903 (m) cc_final: 0.7664 (t) REVERT: T 143 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7644 (mttp) REVERT: U 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7273 (ttpp) REVERT: U 68 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: U 139 SER cc_start: 0.7902 (m) cc_final: 0.7664 (t) REVERT: U 143 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7641 (mttp) REVERT: V 53 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7273 (ttpp) REVERT: V 68 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7462 (tttm) REVERT: V 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7644 (mttm) REVERT: W 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7273 (ttpp) REVERT: W 68 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: W 139 SER cc_start: 0.7903 (m) cc_final: 0.7664 (t) REVERT: W 143 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7642 (mttp) REVERT: X 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7275 (ttpp) REVERT: X 68 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: X 143 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7642 (mttm) outliers start: 24 outliers final: 0 residues processed: 776 average time/residue: 1.7813 time to fit residues: 1584.3142 Evaluate side-chains 667 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 643 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 0.8980 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS D 60 HIS E 60 HIS H 60 HIS M 60 HIS N 60 HIS P 60 HIS V 60 HIS X 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35880 Z= 0.223 Angle : 0.635 5.857 48408 Z= 0.347 Chirality : 0.038 0.126 5016 Planarity : 0.004 0.021 6432 Dihedral : 13.276 178.567 4896 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.24 % Allowed : 7.73 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.12), residues: 4464 helix: 3.75 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.89 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 93 HIS 0.010 0.002 HIS G 60 PHE 0.017 0.002 PHE P 41 TYR 0.020 0.002 TYR J 137 ARG 0.003 0.001 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 734 time to evaluate : 3.250 Fit side-chains REVERT: A 53 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7248 (ttpp) REVERT: A 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7466 (tttm) REVERT: A 139 SER cc_start: 0.7925 (m) cc_final: 0.7704 (t) REVERT: A 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7654 (mttp) REVERT: B 53 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7248 (ttpp) REVERT: B 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7467 (tttm) REVERT: B 139 SER cc_start: 0.7924 (m) cc_final: 0.7713 (t) REVERT: B 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7662 (mttm) REVERT: C 53 LYS cc_start: 0.7648 (ttpp) cc_final: 0.7251 (ttpp) REVERT: C 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: C 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7659 (mttm) REVERT: D 53 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7248 (ttpp) REVERT: D 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7466 (tttm) REVERT: D 139 SER cc_start: 0.7925 (m) cc_final: 0.7704 (t) REVERT: D 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7653 (mttp) REVERT: E 53 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7248 (ttpp) REVERT: E 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: E 139 SER cc_start: 0.7924 (m) cc_final: 0.7703 (t) REVERT: E 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7653 (mttp) REVERT: F 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: F 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: F 139 SER cc_start: 0.7924 (m) cc_final: 0.7704 (t) REVERT: F 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7654 (mttp) REVERT: G 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: G 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: G 139 SER cc_start: 0.7924 (m) cc_final: 0.7703 (t) REVERT: G 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7653 (mttp) REVERT: H 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: H 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7467 (tttm) REVERT: H 139 SER cc_start: 0.7925 (m) cc_final: 0.7704 (t) REVERT: H 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7653 (mttp) REVERT: I 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: I 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: I 139 SER cc_start: 0.7924 (m) cc_final: 0.7704 (t) REVERT: I 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7653 (mttp) REVERT: J 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: J 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7465 (tttm) REVERT: J 139 SER cc_start: 0.7925 (m) cc_final: 0.7704 (t) REVERT: J 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7653 (mttp) REVERT: K 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: K 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7465 (tttm) REVERT: K 139 SER cc_start: 0.7925 (m) cc_final: 0.7704 (t) REVERT: K 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7655 (mttp) REVERT: L 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7249 (ttpp) REVERT: L 68 LYS cc_start: 0.7708 (ttmp) cc_final: 0.7465 (tttm) REVERT: L 139 SER cc_start: 0.7925 (m) cc_final: 0.7704 (t) REVERT: L 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7655 (mttp) REVERT: M 53 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7247 (ttpp) REVERT: M 68 LYS cc_start: 0.7713 (ttmp) cc_final: 0.7470 (tttm) REVERT: M 139 SER cc_start: 0.7924 (m) cc_final: 0.7713 (t) REVERT: M 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7662 (mttm) REVERT: N 53 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7248 (ttpp) REVERT: N 68 LYS cc_start: 0.7712 (ttmp) cc_final: 0.7469 (tttm) REVERT: N 139 SER cc_start: 0.7923 (m) cc_final: 0.7703 (t) REVERT: N 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7654 (mttp) REVERT: O 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7249 (ttpp) REVERT: O 68 LYS cc_start: 0.7708 (ttmp) cc_final: 0.7465 (tttm) REVERT: O 139 SER cc_start: 0.7925 (m) cc_final: 0.7715 (t) REVERT: O 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7661 (mttm) REVERT: P 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: P 68 LYS cc_start: 0.7713 (ttmp) cc_final: 0.7469 (tttm) REVERT: P 139 SER cc_start: 0.7924 (m) cc_final: 0.7704 (t) REVERT: P 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7653 (mttp) REVERT: Q 53 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7248 (ttpp) REVERT: Q 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7467 (tttm) REVERT: Q 139 SER cc_start: 0.7925 (m) cc_final: 0.7714 (t) REVERT: Q 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7662 (mttm) REVERT: R 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: R 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7466 (tttm) REVERT: R 139 SER cc_start: 0.7924 (m) cc_final: 0.7705 (t) REVERT: R 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7654 (mttp) REVERT: S 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7249 (ttpp) REVERT: S 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7466 (tttm) REVERT: S 139 SER cc_start: 0.7924 (m) cc_final: 0.7703 (t) REVERT: S 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7654 (mttp) REVERT: T 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: T 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: T 139 SER cc_start: 0.7924 (m) cc_final: 0.7702 (t) REVERT: T 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7654 (mttp) REVERT: U 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: U 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: U 139 SER cc_start: 0.7924 (m) cc_final: 0.7713 (t) REVERT: U 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7662 (mttm) REVERT: V 53 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7249 (ttpp) REVERT: V 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: V 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7662 (mttm) REVERT: W 53 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7247 (ttpp) REVERT: W 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7467 (tttm) REVERT: W 139 SER cc_start: 0.7925 (m) cc_final: 0.7704 (t) REVERT: W 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7653 (mttp) REVERT: X 53 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7248 (ttpp) REVERT: X 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7465 (tttm) REVERT: X 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7663 (mttm) outliers start: 47 outliers final: 0 residues processed: 757 average time/residue: 1.6390 time to fit residues: 1435.1374 Evaluate side-chains 721 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 721 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 353 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS D 60 HIS E 60 HIS H 60 HIS M 60 HIS N 60 HIS P 60 HIS V 60 HIS X 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 35880 Z= 0.178 Angle : 0.566 5.187 48408 Z= 0.310 Chirality : 0.037 0.128 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.338 179.323 4800 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.24 % Allowed : 7.01 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.05 (0.12), residues: 4464 helix: 3.90 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.84 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP O 93 HIS 0.010 0.002 HIS G 60 PHE 0.016 0.002 PHE O 41 TYR 0.018 0.002 TYR G 137 ARG 0.002 0.000 ARG K 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 724 time to evaluate : 3.250 Fit side-chains REVERT: A 53 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7263 (ttpp) REVERT: A 68 LYS cc_start: 0.7716 (ttmp) cc_final: 0.7475 (tttm) REVERT: A 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: B 53 LYS cc_start: 0.7649 (ttpp) cc_final: 0.7262 (ttpp) REVERT: B 68 LYS cc_start: 0.7714 (ttmp) cc_final: 0.7473 (tttm) REVERT: B 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7665 (mttp) REVERT: B 165 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6938 (tpp) REVERT: C 53 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7267 (ttpp) REVERT: C 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7481 (tttm) REVERT: C 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7671 (mttm) REVERT: D 53 LYS cc_start: 0.7652 (ttpp) cc_final: 0.7265 (ttpp) REVERT: D 68 LYS cc_start: 0.7716 (ttmp) cc_final: 0.7476 (tttm) REVERT: D 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: E 53 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7263 (ttpp) REVERT: E 68 LYS cc_start: 0.7716 (ttmp) cc_final: 0.7476 (tttm) REVERT: E 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: F 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7235 (ttpp) REVERT: F 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7481 (tttm) REVERT: F 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: G 53 LYS cc_start: 0.7627 (ttpp) cc_final: 0.7233 (ttpp) REVERT: G 68 LYS cc_start: 0.7724 (ttmp) cc_final: 0.7483 (tttm) REVERT: G 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: H 53 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7265 (ttpp) REVERT: H 68 LYS cc_start: 0.7717 (ttmp) cc_final: 0.7476 (tttm) REVERT: H 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: I 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7236 (ttpp) REVERT: I 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7480 (tttm) REVERT: I 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: J 53 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7236 (ttpp) REVERT: J 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7483 (tttm) REVERT: J 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: K 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7236 (ttpp) REVERT: K 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: K 143 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7666 (mttp) REVERT: L 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7235 (ttpp) REVERT: L 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: L 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7666 (mttp) REVERT: M 53 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7264 (ttpp) REVERT: M 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7478 (tttm) REVERT: M 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: N 53 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7262 (ttpp) REVERT: N 68 LYS cc_start: 0.7717 (ttmp) cc_final: 0.7476 (tttm) REVERT: N 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: O 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7235 (ttpp) REVERT: O 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: O 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: P 53 LYS cc_start: 0.7652 (ttpp) cc_final: 0.7264 (ttpp) REVERT: P 68 LYS cc_start: 0.7718 (ttmp) cc_final: 0.7477 (tttm) REVERT: P 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: Q 53 LYS cc_start: 0.7627 (ttpp) cc_final: 0.7234 (ttpp) REVERT: Q 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7480 (tttm) REVERT: Q 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7665 (mttp) REVERT: R 53 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7236 (ttpp) REVERT: R 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7478 (tttm) REVERT: R 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: S 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7235 (ttpp) REVERT: S 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: S 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: T 53 LYS cc_start: 0.7627 (ttpp) cc_final: 0.7232 (ttpp) REVERT: T 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7479 (tttm) REVERT: T 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: U 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7235 (ttpp) REVERT: U 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7481 (tttm) REVERT: U 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: V 53 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7263 (ttpp) REVERT: V 68 LYS cc_start: 0.7716 (ttmp) cc_final: 0.7476 (tttm) REVERT: V 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7673 (mttm) REVERT: W 53 LYS cc_start: 0.7627 (ttpp) cc_final: 0.7234 (ttpp) REVERT: W 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7480 (tttm) REVERT: W 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7664 (mttp) REVERT: X 53 LYS cc_start: 0.7652 (ttpp) cc_final: 0.7264 (ttpp) REVERT: X 68 LYS cc_start: 0.7713 (ttmp) cc_final: 0.7473 (tttm) REVERT: X 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7673 (mttm) outliers start: 47 outliers final: 0 residues processed: 747 average time/residue: 1.6781 time to fit residues: 1444.1683 Evaluate side-chains 702 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 701 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 353 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35880 Z= 0.247 Angle : 0.647 5.729 48408 Z= 0.355 Chirality : 0.039 0.128 5016 Planarity : 0.004 0.025 6432 Dihedral : 13.351 179.800 4800 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 6.99 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.78 (0.12), residues: 4464 helix: 3.71 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.72 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP H 93 HIS 0.013 0.002 HIS G 60 PHE 0.020 0.003 PHE X 41 TYR 0.018 0.002 TYR D 137 ARG 0.003 0.001 ARG K 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 724 time to evaluate : 3.212 Fit side-chains REVERT: A 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7254 (ttpp) REVERT: A 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: A 139 SER cc_start: 0.7919 (m) cc_final: 0.7701 (t) REVERT: A 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7685 (mttm) REVERT: A 165 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6954 (tpp) REVERT: B 53 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7254 (ttpp) REVERT: B 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7481 (tttm) REVERT: B 139 SER cc_start: 0.7918 (m) cc_final: 0.7701 (t) REVERT: B 143 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7682 (mttm) REVERT: C 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7256 (ttpp) REVERT: C 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7482 (tttm) REVERT: C 143 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7677 (mttm) REVERT: D 53 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7255 (ttpp) REVERT: D 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7480 (tttm) REVERT: D 139 SER cc_start: 0.7919 (m) cc_final: 0.7703 (t) REVERT: D 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7679 (mttm) REVERT: E 53 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7254 (ttpp) REVERT: E 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7480 (tttm) REVERT: E 139 SER cc_start: 0.7918 (m) cc_final: 0.7701 (t) REVERT: E 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7682 (mttm) REVERT: F 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7256 (ttpp) REVERT: F 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7483 (tttm) REVERT: F 139 SER cc_start: 0.7922 (m) cc_final: 0.7708 (t) REVERT: F 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7679 (mttm) REVERT: G 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7254 (ttpp) REVERT: G 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7481 (tttm) REVERT: G 139 SER cc_start: 0.7922 (m) cc_final: 0.7707 (t) REVERT: G 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7679 (mttm) REVERT: G 165 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6953 (tpp) REVERT: H 53 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7254 (ttpp) REVERT: H 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7480 (tttm) REVERT: H 139 SER cc_start: 0.7919 (m) cc_final: 0.7702 (t) REVERT: H 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7681 (mttm) REVERT: I 53 LYS cc_start: 0.7671 (ttpp) cc_final: 0.7258 (ttpp) REVERT: I 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7482 (tttm) REVERT: I 139 SER cc_start: 0.7922 (m) cc_final: 0.7708 (t) REVERT: I 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7680 (mttm) REVERT: J 53 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7256 (ttpp) REVERT: J 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7480 (tttm) REVERT: J 139 SER cc_start: 0.7923 (m) cc_final: 0.7710 (t) REVERT: J 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7680 (mttm) REVERT: J 165 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: K 53 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7256 (ttpp) REVERT: K 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7480 (tttm) REVERT: K 139 SER cc_start: 0.7923 (m) cc_final: 0.7710 (t) REVERT: K 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7680 (mttm) REVERT: L 53 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7256 (ttpp) REVERT: L 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: L 139 SER cc_start: 0.7923 (m) cc_final: 0.7709 (t) REVERT: L 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7681 (mttm) REVERT: M 53 LYS cc_start: 0.7666 (ttpp) cc_final: 0.7254 (ttpp) REVERT: M 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7483 (tttm) REVERT: M 139 SER cc_start: 0.7917 (m) cc_final: 0.7700 (t) REVERT: M 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7680 (mttm) REVERT: N 53 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7253 (ttpp) REVERT: N 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7482 (tttm) REVERT: N 139 SER cc_start: 0.7917 (m) cc_final: 0.7700 (t) REVERT: N 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7681 (mttm) REVERT: O 53 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7255 (ttpp) REVERT: O 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: O 139 SER cc_start: 0.7923 (m) cc_final: 0.7709 (t) REVERT: O 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7681 (mttm) REVERT: P 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7256 (ttpp) REVERT: P 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7482 (tttm) REVERT: P 139 SER cc_start: 0.7917 (m) cc_final: 0.7701 (t) REVERT: P 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7681 (mttm) REVERT: Q 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7255 (ttpp) REVERT: Q 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7482 (tttm) REVERT: Q 139 SER cc_start: 0.7922 (m) cc_final: 0.7708 (t) REVERT: Q 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7680 (mttm) REVERT: R 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7256 (ttpp) REVERT: R 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7480 (tttm) REVERT: R 139 SER cc_start: 0.7924 (m) cc_final: 0.7709 (t) REVERT: R 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7678 (mttm) REVERT: S 53 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7256 (ttpp) REVERT: S 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7480 (tttm) REVERT: S 139 SER cc_start: 0.7922 (m) cc_final: 0.7708 (t) REVERT: S 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7679 (mttm) REVERT: T 53 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7255 (ttpp) REVERT: T 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7481 (tttm) REVERT: T 139 SER cc_start: 0.7922 (m) cc_final: 0.7707 (t) REVERT: T 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7679 (mttm) REVERT: U 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7255 (ttpp) REVERT: U 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7482 (tttm) REVERT: U 139 SER cc_start: 0.7922 (m) cc_final: 0.7708 (t) REVERT: U 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7679 (mttm) REVERT: V 53 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7254 (ttpp) REVERT: V 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: V 143 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7679 (mttm) REVERT: W 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7254 (ttpp) REVERT: W 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7481 (tttm) REVERT: W 139 SER cc_start: 0.7922 (m) cc_final: 0.7708 (t) REVERT: W 143 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7680 (mttm) REVERT: X 53 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7255 (ttpp) REVERT: X 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: X 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7679 (mttm) outliers start: 48 outliers final: 0 residues processed: 747 average time/residue: 1.6425 time to fit residues: 1418.0829 Evaluate side-chains 725 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 722 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain J residue 165 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.7980 chunk 355 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 394 optimal weight: 1.9990 chunk 327 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS D 60 HIS E 60 HIS H 60 HIS M 60 HIS N 60 HIS P 60 HIS V 60 HIS X 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35880 Z= 0.172 Angle : 0.543 5.043 48408 Z= 0.297 Chirality : 0.036 0.126 5016 Planarity : 0.003 0.019 6432 Dihedral : 13.348 179.823 4800 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 6.99 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.14 (0.12), residues: 4464 helix: 3.97 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.80 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP W 93 HIS 0.012 0.002 HIS W 60 PHE 0.016 0.002 PHE U 41 TYR 0.017 0.002 TYR U 137 ARG 0.002 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 697 time to evaluate : 3.279 Fit side-chains REVERT: A 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7338 (ttpp) REVERT: A 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7466 (tttm) REVERT: A 143 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7679 (mttm) REVERT: A 165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6940 (tpp) REVERT: B 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7338 (ttpp) REVERT: B 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7467 (tttm) REVERT: B 143 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7684 (mttm) REVERT: B 165 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6913 (tpp) REVERT: C 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7339 (ttpp) REVERT: C 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7468 (tttm) REVERT: C 143 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7675 (mttm) REVERT: C 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: D 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7341 (ttpp) REVERT: D 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7465 (tttm) REVERT: D 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7679 (mttm) REVERT: D 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6923 (tpp) REVERT: E 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7338 (ttpp) REVERT: E 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7466 (tttm) REVERT: E 143 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7673 (mttm) REVERT: E 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: F 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7340 (ttpp) REVERT: F 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7470 (tttm) REVERT: F 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7677 (mttm) REVERT: F 165 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6923 (tpp) REVERT: G 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7338 (ttpp) REVERT: G 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7466 (tttm) REVERT: G 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7678 (mttm) REVERT: G 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6923 (tpp) REVERT: H 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7341 (ttpp) REVERT: H 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7466 (tttm) REVERT: H 143 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7684 (mttm) REVERT: H 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: I 53 LYS cc_start: 0.7727 (ttpp) cc_final: 0.7342 (ttpp) REVERT: I 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7470 (tttm) REVERT: I 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7662 (mttp) REVERT: I 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: J 53 LYS cc_start: 0.7728 (ttpp) cc_final: 0.7341 (ttpp) REVERT: J 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: J 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7663 (mttp) REVERT: J 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: K 53 LYS cc_start: 0.7727 (ttpp) cc_final: 0.7342 (ttpp) REVERT: K 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7467 (tttm) REVERT: K 143 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7682 (mttm) REVERT: K 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: L 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7340 (ttpp) REVERT: L 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7467 (tttm) REVERT: L 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7679 (mttm) REVERT: L 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: M 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7340 (ttpp) REVERT: M 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7469 (tttm) REVERT: M 143 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7682 (mttm) REVERT: M 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: N 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7337 (ttpp) REVERT: N 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7468 (tttm) REVERT: N 143 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7683 (mttm) REVERT: N 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: O 53 LYS cc_start: 0.7727 (ttpp) cc_final: 0.7339 (ttpp) REVERT: O 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: O 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7677 (mttm) REVERT: O 165 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: P 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7341 (ttpp) REVERT: P 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7468 (tttm) REVERT: P 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7680 (mttm) REVERT: P 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: Q 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7339 (ttpp) REVERT: Q 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7468 (tttm) REVERT: Q 143 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7678 (mttm) REVERT: Q 165 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: R 53 LYS cc_start: 0.7727 (ttpp) cc_final: 0.7341 (ttpp) REVERT: R 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: R 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7676 (mttm) REVERT: R 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6923 (tpp) REVERT: S 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7340 (ttpp) REVERT: S 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7467 (tttm) REVERT: S 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7677 (mttm) REVERT: S 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: T 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7339 (ttpp) REVERT: T 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7467 (tttm) REVERT: T 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7678 (mttm) REVERT: T 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: U 53 LYS cc_start: 0.7727 (ttpp) cc_final: 0.7340 (ttpp) REVERT: U 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7468 (tttm) REVERT: U 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7677 (mttm) REVERT: U 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: V 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7338 (ttpp) REVERT: V 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7466 (tttm) REVERT: V 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7677 (mttm) REVERT: V 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6924 (tpp) REVERT: W 53 LYS cc_start: 0.7728 (ttpp) cc_final: 0.7339 (ttpp) REVERT: W 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7467 (tttm) REVERT: W 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7678 (mttm) REVERT: W 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6926 (tpp) REVERT: X 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7340 (ttpp) REVERT: X 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7466 (tttm) REVERT: X 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7679 (mttm) REVERT: X 165 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6923 (tpp) outliers start: 48 outliers final: 0 residues processed: 720 average time/residue: 1.6824 time to fit residues: 1396.2654 Evaluate side-chains 711 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 687 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 332 optimal weight: 0.7980 chunk 220 optimal weight: 0.5980 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 0.0870 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 35880 Z= 0.154 Angle : 0.515 4.739 48408 Z= 0.281 Chirality : 0.036 0.127 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.345 179.783 4800 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.66 % Allowed : 7.12 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.31 (0.13), residues: 4464 helix: 4.08 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.89 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP O 93 HIS 0.011 0.002 HIS C 60 PHE 0.014 0.002 PHE P 41 TYR 0.017 0.002 TYR B 137 ARG 0.001 0.000 ARG I 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 712 time to evaluate : 3.276 Fit side-chains REVERT: A 53 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7330 (ttpp) REVERT: A 68 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7455 (tttm) REVERT: A 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7654 (mttm) REVERT: A 165 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6938 (tpp) REVERT: B 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7328 (ttpp) REVERT: B 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7457 (tttm) REVERT: B 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7657 (mttm) REVERT: B 165 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6913 (tpp) REVERT: C 53 LYS cc_start: 0.7709 (ttpp) cc_final: 0.7326 (ttpp) REVERT: C 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7456 (tttm) REVERT: C 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7666 (mttm) REVERT: C 165 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: D 53 LYS cc_start: 0.7717 (ttpp) cc_final: 0.7332 (ttpp) REVERT: D 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7456 (tttm) REVERT: D 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7653 (mttm) REVERT: D 165 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6920 (tpp) REVERT: E 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7328 (ttpp) REVERT: E 68 LYS cc_start: 0.7699 (ttmp) cc_final: 0.7456 (tttm) REVERT: E 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7654 (mttm) REVERT: E 165 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6919 (tpp) REVERT: F 53 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7331 (ttpp) REVERT: F 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7458 (tttm) REVERT: F 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7662 (mttm) REVERT: F 165 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6920 (tpp) REVERT: G 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7327 (ttpp) REVERT: G 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7456 (tttm) REVERT: G 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7663 (mttm) REVERT: G 165 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: H 53 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7332 (ttpp) REVERT: H 68 LYS cc_start: 0.7699 (ttmp) cc_final: 0.7455 (tttm) REVERT: H 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7654 (mttm) REVERT: H 165 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: I 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7331 (ttpp) REVERT: I 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7458 (tttm) REVERT: I 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7667 (mttm) REVERT: I 165 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: J 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7329 (ttpp) REVERT: J 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7457 (tttm) REVERT: J 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7663 (mttm) REVERT: J 165 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: K 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7331 (ttpp) REVERT: K 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: K 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7665 (mttm) REVERT: K 165 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: L 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7328 (ttpp) REVERT: L 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7458 (tttm) REVERT: L 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7665 (mttm) REVERT: L 165 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6918 (tpp) REVERT: M 53 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7330 (ttpp) REVERT: M 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7456 (tttm) REVERT: M 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7653 (mttm) REVERT: M 165 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6919 (tpp) REVERT: N 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7327 (ttpp) REVERT: N 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7456 (tttm) REVERT: N 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7654 (mttm) REVERT: N 165 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: O 53 LYS cc_start: 0.7710 (ttpp) cc_final: 0.7325 (ttpp) REVERT: O 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7458 (tttm) REVERT: O 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7663 (mttm) REVERT: O 165 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: P 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7330 (ttpp) REVERT: P 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7456 (tttm) REVERT: P 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7655 (mttm) REVERT: P 165 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6919 (tpp) REVERT: Q 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7329 (ttpp) REVERT: Q 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7459 (tttm) REVERT: Q 143 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7664 (mttm) REVERT: Q 165 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6922 (tpp) REVERT: R 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7329 (ttpp) REVERT: R 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7457 (tttm) REVERT: R 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7663 (mttm) REVERT: R 165 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6920 (tpp) REVERT: S 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7329 (ttpp) REVERT: S 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: S 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7664 (mttm) REVERT: S 165 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: T 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7329 (ttpp) REVERT: T 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7458 (tttm) REVERT: T 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7663 (mttm) REVERT: T 165 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: U 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7329 (ttpp) REVERT: U 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7457 (tttm) REVERT: U 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7662 (mttm) REVERT: U 165 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6921 (tpp) REVERT: V 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7328 (ttpp) REVERT: V 68 LYS cc_start: 0.7699 (ttmp) cc_final: 0.7456 (tttm) REVERT: V 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7654 (mttm) REVERT: V 165 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6918 (tpp) REVERT: W 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7328 (ttpp) REVERT: W 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7457 (tttm) REVERT: W 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7664 (mttm) REVERT: W 165 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6919 (tpp) REVERT: X 53 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7331 (ttpp) REVERT: X 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7456 (tttm) REVERT: X 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7654 (mttm) REVERT: X 165 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6917 (tpp) outliers start: 25 outliers final: 0 residues processed: 713 average time/residue: 1.7306 time to fit residues: 1417.4971 Evaluate side-chains 718 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 694 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 250 optimal weight: 0.8980 chunk 267 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 GLN ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 GLN ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 141 GLN ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 GLN ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 141 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35880 Z= 0.232 Angle : 0.605 5.532 48408 Z= 0.333 Chirality : 0.038 0.129 5016 Planarity : 0.004 0.027 6432 Dihedral : 13.302 179.538 4800 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 8.10 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.89 (0.12), residues: 4464 helix: 3.78 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.76 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 93 HIS 0.013 0.002 HIS X 60 PHE 0.018 0.003 PHE I 41 TYR 0.018 0.002 TYR R 137 ARG 0.002 0.001 ARG I 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 702 time to evaluate : 3.284 Fit side-chains REVERT: A 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7261 (ttpp) REVERT: A 68 LYS cc_start: 0.7694 (ttmp) cc_final: 0.7467 (tttm) REVERT: A 143 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7667 (mttm) REVERT: A 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6963 (tpp) REVERT: B 53 LYS cc_start: 0.7679 (ttpp) cc_final: 0.7259 (ttpp) REVERT: B 68 LYS cc_start: 0.7694 (ttmp) cc_final: 0.7469 (tttm) REVERT: B 143 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7665 (mttm) REVERT: B 165 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: C 53 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7253 (ttpp) REVERT: C 68 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7473 (tttm) REVERT: C 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7668 (mttm) REVERT: C 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: D 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7263 (ttpp) REVERT: D 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7469 (tttm) REVERT: D 143 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7666 (mttm) REVERT: D 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6993 (tpp) REVERT: E 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7261 (ttpp) REVERT: E 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7469 (tttm) REVERT: E 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7674 (mttm) REVERT: E 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6994 (tpp) REVERT: F 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7264 (ttpp) REVERT: F 68 LYS cc_start: 0.7697 (ttmp) cc_final: 0.7473 (tttm) REVERT: F 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7673 (mttm) REVERT: F 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6994 (tpp) REVERT: G 53 LYS cc_start: 0.7661 (ttpp) cc_final: 0.7240 (ttpp) REVERT: G 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7470 (tttm) REVERT: G 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7674 (mttm) REVERT: G 165 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6987 (tpp) REVERT: H 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7262 (ttpp) REVERT: H 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7469 (tttm) REVERT: H 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7666 (mttm) REVERT: H 165 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6991 (tpp) REVERT: I 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7263 (ttpp) REVERT: I 68 LYS cc_start: 0.7696 (ttmp) cc_final: 0.7471 (tttm) REVERT: I 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7674 (mttm) REVERT: I 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: J 53 LYS cc_start: 0.7662 (ttpp) cc_final: 0.7240 (ttpp) REVERT: J 68 LYS cc_start: 0.7696 (ttmp) cc_final: 0.7470 (tttm) REVERT: J 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7674 (mttm) REVERT: J 165 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6985 (tpp) REVERT: K 53 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7264 (ttpp) REVERT: K 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7470 (tttm) REVERT: K 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7675 (mttm) REVERT: K 165 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6990 (tpp) REVERT: L 53 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7262 (ttpp) REVERT: L 68 LYS cc_start: 0.7694 (ttmp) cc_final: 0.7469 (tttm) REVERT: L 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7676 (mttm) REVERT: L 165 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6993 (tpp) REVERT: M 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7263 (ttpp) REVERT: M 68 LYS cc_start: 0.7697 (ttmp) cc_final: 0.7471 (tttm) REVERT: M 143 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7665 (mttm) REVERT: M 165 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6993 (tpp) REVERT: N 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7261 (ttpp) REVERT: N 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7470 (tttm) REVERT: N 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7665 (mttm) REVERT: N 165 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6994 (tpp) REVERT: O 53 LYS cc_start: 0.7661 (ttpp) cc_final: 0.7239 (ttpp) REVERT: O 68 LYS cc_start: 0.7694 (ttmp) cc_final: 0.7469 (tttm) REVERT: O 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7675 (mttm) REVERT: O 165 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: P 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7264 (ttpp) REVERT: P 68 LYS cc_start: 0.7696 (ttmp) cc_final: 0.7471 (tttm) REVERT: P 143 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7675 (mttm) REVERT: P 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: Q 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7262 (ttpp) REVERT: Q 68 LYS cc_start: 0.7694 (ttmp) cc_final: 0.7470 (tttm) REVERT: Q 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7675 (mttm) REVERT: Q 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: R 53 LYS cc_start: 0.7661 (ttpp) cc_final: 0.7240 (ttpp) REVERT: R 68 LYS cc_start: 0.7696 (ttmp) cc_final: 0.7470 (tttm) REVERT: R 143 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7672 (mttm) REVERT: R 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6993 (tpp) REVERT: S 53 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7264 (ttpp) REVERT: S 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7470 (tttm) REVERT: S 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7675 (mttm) REVERT: S 165 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6993 (tpp) REVERT: T 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7263 (ttpp) REVERT: T 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7471 (tttm) REVERT: T 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7673 (mttm) REVERT: T 165 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6994 (tpp) REVERT: U 53 LYS cc_start: 0.7662 (ttpp) cc_final: 0.7242 (ttpp) REVERT: U 68 LYS cc_start: 0.7697 (ttmp) cc_final: 0.7472 (tttm) REVERT: U 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7674 (mttm) REVERT: U 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6994 (tpp) REVERT: V 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7261 (ttpp) REVERT: V 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7469 (tttm) REVERT: V 143 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7675 (mttm) REVERT: V 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6994 (tpp) REVERT: W 53 LYS cc_start: 0.7661 (ttpp) cc_final: 0.7240 (ttpp) REVERT: W 68 LYS cc_start: 0.7695 (ttmp) cc_final: 0.7470 (tttm) REVERT: W 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7651 (mttp) REVERT: W 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: X 53 LYS cc_start: 0.7679 (ttpp) cc_final: 0.7259 (ttpp) REVERT: X 68 LYS cc_start: 0.7694 (ttmp) cc_final: 0.7469 (tttm) REVERT: X 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7675 (mttm) REVERT: X 165 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6992 (tpp) outliers start: 24 outliers final: 0 residues processed: 702 average time/residue: 1.7827 time to fit residues: 1443.6726 Evaluate side-chains 726 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 702 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.5980 chunk 376 optimal weight: 7.9990 chunk 343 optimal weight: 2.9990 chunk 366 optimal weight: 0.9980 chunk 220 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 331 optimal weight: 0.5980 chunk 346 optimal weight: 2.9990 chunk 365 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 65 HIS D 65 HIS E 65 HIS H 65 HIS M 65 HIS N 65 HIS P 65 HIS V 65 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35880 Z= 0.165 Angle : 0.526 4.812 48408 Z= 0.287 Chirality : 0.036 0.128 5016 Planarity : 0.003 0.019 6432 Dihedral : 13.326 179.729 4800 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 7.65 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.18 (0.13), residues: 4464 helix: 3.97 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.95 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP F 93 HIS 0.012 0.002 HIS E 60 PHE 0.015 0.002 PHE D 41 TYR 0.016 0.002 TYR R 137 ARG 0.001 0.000 ARG G 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 721 time to evaluate : 3.264 Fit side-chains REVERT: A 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7332 (ttpp) REVERT: A 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7457 (tttm) REVERT: A 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7661 (mttm) REVERT: A 165 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: B 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7330 (ttpp) REVERT: B 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7458 (tttm) REVERT: B 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7656 (mttm) REVERT: B 165 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: C 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7333 (ttpp) REVERT: C 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7459 (tttm) REVERT: C 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7657 (mttm) REVERT: C 165 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7002 (tpp) REVERT: D 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7332 (ttpp) REVERT: D 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7457 (tttm) REVERT: D 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7659 (mttm) REVERT: D 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: E 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7330 (ttpp) REVERT: E 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7457 (tttm) REVERT: E 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7660 (mttm) REVERT: E 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7001 (tpp) REVERT: F 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7333 (ttpp) REVERT: F 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7459 (tttm) REVERT: F 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7659 (mttm) REVERT: F 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7000 (tpp) REVERT: G 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7329 (ttpp) REVERT: G 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7458 (tttm) REVERT: G 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7660 (mttm) REVERT: G 165 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: H 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7332 (ttpp) REVERT: H 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7457 (tttm) REVERT: H 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7660 (mttm) REVERT: H 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6949 (tpp) REVERT: I 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7333 (ttpp) REVERT: I 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7457 (tttm) REVERT: I 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7656 (mttm) REVERT: I 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6949 (tpp) REVERT: J 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7332 (ttpp) REVERT: J 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7458 (tttm) REVERT: J 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7660 (mttm) REVERT: J 165 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6931 (tpp) REVERT: K 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7334 (ttpp) REVERT: K 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: K 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7658 (mttm) REVERT: K 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6949 (tpp) REVERT: L 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7332 (ttpp) REVERT: L 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: L 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7657 (mttm) REVERT: L 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7002 (tpp) REVERT: M 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7332 (ttpp) REVERT: M 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7457 (tttm) REVERT: M 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7659 (mttm) REVERT: M 165 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: N 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7329 (ttpp) REVERT: N 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7457 (tttm) REVERT: N 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7654 (mttm) REVERT: N 165 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: O 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7330 (ttpp) REVERT: O 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: O 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7661 (mttm) REVERT: O 165 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: P 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7332 (ttpp) REVERT: P 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7457 (tttm) REVERT: P 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7661 (mttm) REVERT: P 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6948 (tpp) REVERT: Q 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7331 (ttpp) REVERT: Q 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7458 (tttm) REVERT: Q 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7656 (mttm) REVERT: Q 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7002 (tpp) REVERT: R 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7332 (ttpp) REVERT: R 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7458 (tttm) REVERT: R 143 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7656 (mttm) REVERT: R 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: S 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7331 (ttpp) REVERT: S 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: S 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7660 (mttm) REVERT: S 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: T 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7331 (ttpp) REVERT: T 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7458 (tttm) REVERT: T 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7660 (mttm) REVERT: T 165 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7001 (tpp) REVERT: U 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7332 (ttpp) REVERT: U 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7458 (tttm) REVERT: U 143 LYS cc_start: 0.7963 (ttmm) cc_final: 0.7660 (mttm) REVERT: U 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: V 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7331 (ttpp) REVERT: V 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7457 (tttm) REVERT: V 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7658 (mttm) REVERT: V 165 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: W 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7330 (ttpp) REVERT: W 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7458 (tttm) REVERT: W 143 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7656 (mttm) REVERT: W 165 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7002 (tpp) REVERT: X 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7334 (ttpp) REVERT: X 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7458 (tttm) REVERT: X 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7660 (mttm) REVERT: X 165 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6950 (tpp) outliers start: 24 outliers final: 0 residues processed: 721 average time/residue: 1.7593 time to fit residues: 1455.8275 Evaluate side-chains 728 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 704 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 5.9990 chunk 236 optimal weight: 0.1980 chunk 183 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 406 optimal weight: 1.9990 chunk 374 optimal weight: 1.9990 chunk 323 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 198 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 65 HIS D 65 HIS E 65 HIS H 65 HIS M 65 HIS N 65 HIS P 65 HIS V 65 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35880 Z= 0.172 Angle : 0.539 4.887 48408 Z= 0.295 Chirality : 0.036 0.131 5016 Planarity : 0.003 0.027 6432 Dihedral : 13.306 179.606 4800 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.24 % Allowed : 7.52 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.15 (0.13), residues: 4464 helix: 3.94 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.99 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 93 HIS 0.004 0.001 HIS E 60 PHE 0.015 0.002 PHE T 41 TYR 0.017 0.002 TYR Q 137 ARG 0.001 0.000 ARG D 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 702 time to evaluate : 3.289 Fit side-chains REVERT: A 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7335 (ttpp) REVERT: A 68 LYS cc_start: 0.7697 (ttmp) cc_final: 0.7456 (tttm) REVERT: A 140 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6668 (pp20) REVERT: A 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7652 (mttm) REVERT: A 165 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6979 (tpp) REVERT: B 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7332 (ttpp) REVERT: B 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7457 (tttm) REVERT: B 140 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6671 (pp20) REVERT: B 143 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7654 (mttm) REVERT: B 165 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7029 (tpp) REVERT: C 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7335 (ttpp) REVERT: C 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7458 (tttm) REVERT: C 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7659 (mttm) REVERT: C 165 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7027 (tpp) REVERT: D 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7334 (ttpp) REVERT: D 68 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7456 (tttm) REVERT: D 140 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6669 (pp20) REVERT: D 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7652 (mttm) REVERT: D 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: E 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7333 (ttpp) REVERT: E 68 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7456 (tttm) REVERT: E 140 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6670 (pp20) REVERT: E 143 LYS cc_start: 0.7963 (ttmm) cc_final: 0.7652 (mttm) REVERT: E 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: F 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7336 (ttpp) REVERT: F 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7459 (tttm) REVERT: F 140 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6669 (pp20) REVERT: F 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7653 (mttm) REVERT: F 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: G 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7331 (ttpp) REVERT: G 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: G 140 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6669 (pp20) REVERT: G 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7653 (mttm) REVERT: G 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6970 (tpp) REVERT: H 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7334 (ttpp) REVERT: H 68 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7456 (tttm) REVERT: H 140 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6668 (pp20) REVERT: H 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7653 (mttm) REVERT: H 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7027 (tpp) REVERT: I 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7336 (ttpp) REVERT: I 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7459 (tttm) REVERT: I 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7657 (mttm) REVERT: I 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7027 (tpp) REVERT: J 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7335 (ttpp) REVERT: J 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7457 (tttm) REVERT: J 140 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6668 (pp20) REVERT: J 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7653 (mttm) REVERT: J 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: K 53 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7336 (ttpp) REVERT: K 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7458 (tttm) REVERT: K 140 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6656 (pp20) REVERT: K 143 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7651 (mttm) REVERT: K 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: L 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7334 (ttpp) REVERT: L 68 LYS cc_start: 0.7699 (ttmp) cc_final: 0.7458 (tttm) REVERT: L 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7657 (mttm) REVERT: L 165 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7027 (tpp) REVERT: M 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7334 (ttpp) REVERT: M 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7457 (tttm) REVERT: M 140 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6670 (pp20) REVERT: M 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7653 (mttm) REVERT: M 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: N 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7331 (ttpp) REVERT: N 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7457 (tttm) REVERT: N 140 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6669 (pp20) REVERT: N 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7653 (mttm) REVERT: N 165 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: O 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7333 (ttpp) REVERT: O 68 LYS cc_start: 0.7699 (ttmp) cc_final: 0.7457 (tttm) REVERT: O 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7656 (mttm) REVERT: O 165 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7028 (tpp) REVERT: P 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7334 (ttpp) REVERT: P 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7457 (tttm) REVERT: P 140 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6670 (pp20) REVERT: P 143 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7654 (mttm) REVERT: P 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7027 (tpp) REVERT: Q 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7334 (ttpp) REVERT: Q 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: Q 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7658 (mttm) REVERT: Q 165 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7027 (tpp) REVERT: R 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7334 (ttpp) REVERT: R 68 LYS cc_start: 0.7699 (ttmp) cc_final: 0.7457 (tttm) REVERT: R 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7657 (mttm) REVERT: R 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: S 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7334 (ttpp) REVERT: S 68 LYS cc_start: 0.7699 (ttmp) cc_final: 0.7458 (tttm) REVERT: S 140 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6669 (pp20) REVERT: S 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7653 (mttm) REVERT: S 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: T 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7333 (ttpp) REVERT: T 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7458 (tttm) REVERT: T 143 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7658 (mttm) REVERT: T 165 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: U 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7334 (ttpp) REVERT: U 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7459 (tttm) REVERT: U 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7661 (mttm) REVERT: U 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: V 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7332 (ttpp) REVERT: V 68 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7457 (tttm) REVERT: V 143 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7659 (mttm) REVERT: V 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) REVERT: W 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7332 (ttpp) REVERT: W 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: W 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7657 (mttm) REVERT: W 165 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7027 (tpp) REVERT: X 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7335 (ttpp) REVERT: X 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7458 (tttm) REVERT: X 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7660 (mttm) REVERT: X 165 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7026 (tpp) outliers start: 47 outliers final: 0 residues processed: 725 average time/residue: 1.6989 time to fit residues: 1419.9326 Evaluate side-chains 726 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 702 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 7.9990 chunk 344 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 332 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 65 HIS D 65 HIS E 65 HIS F 60 HIS F 65 HIS G 65 HIS H 65 HIS I 60 HIS I 65 HIS J 65 HIS K 60 HIS K 65 HIS L 60 HIS L 65 HIS M 65 HIS N 65 HIS ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 HIS P 65 HIS Q 60 HIS Q 65 HIS ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 HIS S 60 HIS S 65 HIS T 60 HIS T 65 HIS ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 HIS V 65 HIS W 60 HIS W 65 HIS ** X 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.149826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.136674 restraints weight = 163200.801| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.61 r_work: 0.3116 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work: 0.2888 rms_B_bonded: 4.15 restraints_weight: 0.1250 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35880 Z= 0.220 Angle : 0.594 5.390 48408 Z= 0.327 Chirality : 0.037 0.133 5016 Planarity : 0.004 0.036 6432 Dihedral : 13.252 179.570 4800 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.24 % Allowed : 7.52 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.87 (0.12), residues: 4464 helix: 3.75 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP N 93 HIS 0.016 0.002 HIS A 60 PHE 0.018 0.002 PHE W 41 TYR 0.016 0.002 TYR R 137 ARG 0.002 0.001 ARG F 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20523.19 seconds wall clock time: 357 minutes 26.53 seconds (21446.53 seconds total)