Starting phenix.real_space_refine on Sun Oct 13 09:00:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/10_2024/8en7_28269.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/10_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_28269/10_2024/8en7_28269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/10_2024/8en7_28269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/10_2024/8en7_28269.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/10_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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 31.19, per 1000 atoms: 0.83 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: 9.04 Conformation dependent library (CDL) restraints added in 7.4 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: 2.27 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: 12.17 Time building geometry restraints manager: 10.47 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: 9.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.030 Extract box with map and model: 1.380 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 90.090 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.230 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:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.540 ------------------------------------------------------------------------------- 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 : 3.153 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: 2.0540 time to fit residues: 2039.4906 Evaluate side-chains 760 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 736 time to evaluate : 4.014 ------------------------------------------------------------------------------- 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 : 4.151 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: 2.0986 time to fit residues: 1866.4653 Evaluate side-chains 667 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 643 time to evaluate : 4.287 ------------------------------------------------------------------------------- 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: 0.5980 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 0.7980 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 60 HIS V 60 HIS X 60 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35880 Z= 0.221 Angle : 0.633 5.853 48408 Z= 0.346 Chirality : 0.038 0.126 5016 Planarity : 0.004 0.021 6432 Dihedral : 13.277 178.578 4896 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.59 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: 4.89 (0.12), residues: 4464 helix: 3.76 (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 M 93 HIS 0.010 0.002 HIS J 60 PHE 0.017 0.002 PHE X 41 TYR 0.020 0.002 TYR J 137 ARG 0.003 0.001 ARG X 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 780 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 733 time to evaluate : 4.049 Fit side-chains REVERT: A 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (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: 0.7644 (ttpp) cc_final: 0.7246 (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: 0.7703 (t) REVERT: B 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7654 (mttp) REVERT: C 53 LYS cc_start: 0.7648 (ttpp) cc_final: 0.7251 (ttpp) REVERT: C 68 LYS cc_start: 0.7712 (ttmp) cc_final: 0.7469 (tttm) REVERT: C 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7660 (mttm) REVERT: D 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (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: 0.7714 (t) REVERT: D 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7660 (mttm) REVERT: E 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (ttpp) REVERT: E 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: E 139 SER cc_start: 0.7923 (m) cc_final: 0.7702 (t) REVERT: E 143 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7652 (mttp) REVERT: F 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7246 (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: 0.7713 (t) REVERT: F 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7662 (mttm) REVERT: G 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (ttpp) REVERT: G 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7467 (tttm) REVERT: G 139 SER cc_start: 0.7923 (m) cc_final: 0.7702 (t) REVERT: G 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7653 (mttp) REVERT: H 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (ttpp) REVERT: H 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7467 (tttm) REVERT: H 139 SER cc_start: 0.7924 (m) cc_final: 0.7703 (t) REVERT: H 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7653 (mttp) REVERT: I 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7246 (ttpp) REVERT: I 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: I 139 SER cc_start: 0.7923 (m) cc_final: 0.7703 (t) REVERT: I 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7653 (mttp) REVERT: J 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (ttpp) REVERT: J 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7466 (tttm) REVERT: J 139 SER cc_start: 0.7924 (m) cc_final: 0.7703 (t) REVERT: J 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7653 (mttp) REVERT: K 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (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: 0.7714 (t) REVERT: K 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7663 (mttm) REVERT: L 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (ttpp) REVERT: L 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7465 (tttm) REVERT: L 139 SER cc_start: 0.7925 (m) cc_final: 0.7715 (t) REVERT: L 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7663 (mttm) REVERT: M 53 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7246 (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: 0.7644 (ttpp) cc_final: 0.7247 (ttpp) REVERT: N 68 LYS cc_start: 0.7712 (ttmp) cc_final: 0.7468 (tttm) REVERT: N 139 SER cc_start: 0.7924 (m) cc_final: 0.7702 (t) REVERT: N 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7653 (mttp) REVERT: O 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (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: 0.7972 (ttmm) cc_final: 0.7661 (mttm) REVERT: P 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (ttpp) REVERT: P 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: P 139 SER cc_start: 0.7923 (m) cc_final: 0.7703 (t) REVERT: P 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7654 (mttp) REVERT: Q 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (ttpp) REVERT: Q 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7468 (tttm) REVERT: Q 139 SER cc_start: 0.7924 (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: 0.7645 (ttpp) cc_final: 0.7246 (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: 0.7714 (t) REVERT: R 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7661 (mttm) REVERT: S 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (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: 0.7702 (t) REVERT: S 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7653 (mttp) REVERT: T 53 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7246 (ttpp) REVERT: T 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7467 (tttm) REVERT: T 139 SER cc_start: 0.7923 (m) cc_final: 0.7712 (t) REVERT: T 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7662 (mttm) REVERT: U 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7246 (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: 0.7703 (t) REVERT: U 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7654 (mttp) REVERT: V 53 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7247 (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: 0.7644 (ttpp) cc_final: 0.7247 (ttpp) REVERT: W 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7467 (tttm) REVERT: W 139 SER cc_start: 0.7924 (m) cc_final: 0.7714 (t) REVERT: W 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7662 (mttm) REVERT: X 53 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7247 (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: 756 average time/residue: 1.8217 time to fit residues: 1590.7554 Evaluate side-chains 721 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 721 time to evaluate : 3.008 ------------------------------------------------------------------------------- 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: 0.6980 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 353 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.2399 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= 0.179 Angle : 0.569 5.224 48408 Z= 0.311 Chirality : 0.037 0.128 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.342 179.376 4800 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.91 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: 5.04 (0.12), residues: 4464 helix: 3.89 (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 E 93 HIS 0.010 0.002 HIS G 60 PHE 0.016 0.002 PHE E 41 TYR 0.018 0.002 TYR K 137 ARG 0.002 0.000 ARG U 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 764 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 717 time to evaluate : 3.910 Fit side-chains REVERT: A 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7235 (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: 0.7653 (ttpp) cc_final: 0.7265 (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: 0.7664 (mttp) REVERT: B 165 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6939 (tpp) REVERT: C 53 LYS cc_start: 0.7630 (ttpp) cc_final: 0.7238 (ttpp) REVERT: C 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7481 (tttm) REVERT: C 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7673 (mttm) REVERT: D 53 LYS cc_start: 0.7630 (ttpp) cc_final: 0.7238 (ttpp) REVERT: D 68 LYS cc_start: 0.7716 (ttmp) cc_final: 0.7475 (tttm) REVERT: D 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7663 (mttp) REVERT: E 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7235 (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: 0.7630 (ttpp) cc_final: 0.7236 (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: 0.7663 (mttp) REVERT: G 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7234 (ttpp) REVERT: G 68 LYS cc_start: 0.7723 (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: 0.7628 (ttpp) cc_final: 0.7237 (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: 0.7663 (mttp) REVERT: I 53 LYS cc_start: 0.7630 (ttpp) cc_final: 0.7237 (ttpp) REVERT: I 68 LYS cc_start: 0.7720 (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: 0.7724 (ttmp) cc_final: 0.7484 (tttm) REVERT: J 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: K 53 LYS cc_start: 0.7629 (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: 0.7980 (ttmm) cc_final: 0.7666 (mttp) REVERT: L 53 LYS cc_start: 0.7629 (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: 0.7629 (ttpp) cc_final: 0.7237 (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: 0.7663 (mttp) REVERT: N 53 LYS cc_start: 0.7627 (ttpp) cc_final: 0.7235 (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: 0.7629 (ttpp) cc_final: 0.7236 (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: 0.7629 (ttpp) cc_final: 0.7238 (ttpp) REVERT: P 68 LYS cc_start: 0.7718 (ttmp) cc_final: 0.7478 (tttm) REVERT: P 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: Q 53 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7235 (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: 0.7664 (mttp) REVERT: R 53 LYS cc_start: 0.7630 (ttpp) cc_final: 0.7236 (ttpp) REVERT: R 68 LYS cc_start: 0.7718 (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: 0.7630 (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: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: T 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7233 (ttpp) REVERT: T 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7479 (tttm) REVERT: T 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7664 (mttp) REVERT: U 53 LYS cc_start: 0.7630 (ttpp) cc_final: 0.7237 (ttpp) REVERT: U 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7481 (tttm) REVERT: U 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7663 (mttp) REVERT: V 53 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7235 (ttpp) REVERT: V 68 LYS cc_start: 0.7716 (ttmp) cc_final: 0.7475 (tttm) REVERT: V 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7675 (mttm) REVERT: W 53 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7235 (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: 0.7655 (ttpp) cc_final: 0.7268 (ttpp) REVERT: X 68 LYS cc_start: 0.7713 (ttmp) cc_final: 0.7472 (tttm) REVERT: X 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7673 (mttm) outliers start: 47 outliers final: 0 residues processed: 740 average time/residue: 1.6381 time to fit residues: 1395.4388 Evaluate side-chains 702 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 701 time to evaluate : 3.080 ------------------------------------------------------------------------------- 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: 0.9980 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 353 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.2442 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= 0.219 Angle : 0.612 5.557 48408 Z= 0.337 Chirality : 0.038 0.127 5016 Planarity : 0.004 0.022 6432 Dihedral : 13.363 179.875 4800 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.75 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: 4.87 (0.12), residues: 4464 helix: 3.77 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.75 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP S 93 HIS 0.012 0.002 HIS O 60 PHE 0.019 0.002 PHE D 41 TYR 0.018 0.002 TYR M 137 ARG 0.003 0.001 ARG T 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 765 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 717 time to evaluate : 3.141 Fit side-chains REVERT: A 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7261 (ttpp) REVERT: A 68 LYS cc_start: 0.7724 (ttmp) cc_final: 0.7484 (tttm) REVERT: A 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7676 (mttm) REVERT: A 165 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: B 53 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7261 (ttpp) REVERT: B 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7486 (tttm) REVERT: B 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7676 (mttm) REVERT: C 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7262 (ttpp) REVERT: C 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7486 (tttm) REVERT: C 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7677 (mttm) REVERT: C 165 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6957 (tpp) REVERT: D 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7263 (ttpp) REVERT: D 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7484 (tttm) REVERT: D 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7674 (mttm) REVERT: D 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6949 (tpp) REVERT: E 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7261 (ttpp) REVERT: E 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7484 (tttm) REVERT: E 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7676 (mttm) REVERT: E 165 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: F 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7262 (ttpp) REVERT: F 68 LYS cc_start: 0.7724 (ttmp) cc_final: 0.7487 (tttm) REVERT: F 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7675 (mttm) REVERT: F 165 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6954 (tpp) REVERT: G 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7261 (ttpp) REVERT: G 68 LYS cc_start: 0.7724 (ttmp) cc_final: 0.7486 (tttm) REVERT: G 139 SER cc_start: 0.7889 (m) cc_final: 0.7675 (t) REVERT: G 143 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7678 (mttm) REVERT: G 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: H 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7262 (ttpp) REVERT: H 68 LYS cc_start: 0.7725 (ttmp) cc_final: 0.7485 (tttm) REVERT: H 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7675 (mttm) REVERT: H 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6949 (tpp) REVERT: I 53 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7263 (ttpp) REVERT: I 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7486 (tttm) REVERT: I 143 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7676 (mttm) REVERT: I 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: J 53 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7262 (ttpp) REVERT: J 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7484 (tttm) REVERT: J 139 SER cc_start: 0.7891 (m) cc_final: 0.7679 (t) REVERT: J 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7677 (mttm) REVERT: J 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: K 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7261 (ttpp) REVERT: K 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7483 (tttm) REVERT: K 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7676 (mttm) REVERT: K 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: L 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7260 (ttpp) REVERT: L 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7483 (tttm) REVERT: L 143 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7678 (mttm) REVERT: L 165 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6953 (tpp) REVERT: M 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7262 (ttpp) REVERT: M 68 LYS cc_start: 0.7728 (ttmp) cc_final: 0.7489 (tttm) REVERT: M 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7675 (mttm) REVERT: M 165 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6954 (tpp) REVERT: N 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7262 (ttpp) REVERT: N 68 LYS cc_start: 0.7726 (ttmp) cc_final: 0.7487 (tttm) REVERT: N 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7676 (mttm) REVERT: N 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: O 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7261 (ttpp) REVERT: O 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7483 (tttm) REVERT: O 139 SER cc_start: 0.7891 (m) cc_final: 0.7678 (t) REVERT: O 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7677 (mttm) REVERT: O 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: P 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7263 (ttpp) REVERT: P 68 LYS cc_start: 0.7724 (ttmp) cc_final: 0.7486 (tttm) REVERT: P 143 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7676 (mttm) REVERT: P 165 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6953 (tpp) REVERT: Q 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7260 (ttpp) REVERT: Q 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7485 (tttm) REVERT: Q 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7676 (mttm) REVERT: Q 165 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: R 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7262 (ttpp) REVERT: R 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7484 (tttm) REVERT: R 139 SER cc_start: 0.7891 (m) cc_final: 0.7678 (t) REVERT: R 143 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7676 (mttm) REVERT: R 165 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6946 (tpp) REVERT: S 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7261 (ttpp) REVERT: S 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7484 (tttm) REVERT: S 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7676 (mttm) REVERT: S 165 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6947 (tpp) REVERT: T 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7260 (ttpp) REVERT: T 68 LYS cc_start: 0.7724 (ttmp) cc_final: 0.7486 (tttm) REVERT: T 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7676 (mttm) REVERT: T 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: U 53 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7263 (ttpp) REVERT: U 68 LYS cc_start: 0.7725 (ttmp) cc_final: 0.7487 (tttm) REVERT: U 139 SER cc_start: 0.7890 (m) cc_final: 0.7677 (t) REVERT: U 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7677 (mttm) REVERT: U 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: V 53 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7261 (ttpp) REVERT: V 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7483 (tttm) REVERT: V 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7679 (mttm) REVERT: V 165 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6953 (tpp) REVERT: W 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7261 (ttpp) REVERT: W 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7485 (tttm) REVERT: W 139 SER cc_start: 0.7891 (m) cc_final: 0.7677 (t) REVERT: W 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7678 (mttm) REVERT: W 165 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: X 53 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7263 (ttpp) REVERT: X 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7484 (tttm) REVERT: X 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7678 (mttm) REVERT: X 165 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6953 (tpp) outliers start: 48 outliers final: 0 residues processed: 740 average time/residue: 1.6515 time to fit residues: 1408.2915 Evaluate side-chains 730 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 707 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.9980 chunk 355 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 394 optimal weight: 1.9990 chunk 327 optimal weight: 0.5980 chunk 182 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7624 moved from start: 0.2539 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= 0.168 Angle : 0.537 5.018 48408 Z= 0.294 Chirality : 0.036 0.126 5016 Planarity : 0.003 0.019 6432 Dihedral : 13.349 179.797 4800 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.29 % Allowed : 6.96 % 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: 5.17 (0.12), residues: 4464 helix: 3.98 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.86 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 93 HIS 0.013 0.002 HIS W 60 PHE 0.015 0.002 PHE C 41 TYR 0.017 0.002 TYR G 137 ARG 0.001 0.000 ARG D 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 753 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 704 time to evaluate : 3.268 Fit side-chains REVERT: A 53 LYS cc_start: 0.7719 (ttpp) cc_final: 0.7336 (ttpp) REVERT: A 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7464 (tttm) REVERT: A 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7673 (mttm) REVERT: A 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: B 53 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7337 (ttpp) REVERT: B 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7466 (tttm) REVERT: B 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7679 (mttm) REVERT: B 165 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6911 (tpp) REVERT: C 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7337 (ttpp) REVERT: C 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7468 (tttm) REVERT: C 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7681 (mttm) REVERT: C 165 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: D 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7338 (ttpp) REVERT: D 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: D 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7673 (mttm) REVERT: D 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: E 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7336 (ttpp) REVERT: E 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: E 143 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7677 (mttm) REVERT: E 165 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6923 (tpp) REVERT: F 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7338 (ttpp) REVERT: F 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7468 (tttm) REVERT: F 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7673 (mttm) REVERT: F 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: G 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7336 (ttpp) REVERT: G 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7465 (tttm) REVERT: G 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7660 (mttp) REVERT: G 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: H 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7338 (ttpp) REVERT: H 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: H 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7681 (mttm) REVERT: H 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: I 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7337 (ttpp) REVERT: I 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7467 (tttm) REVERT: I 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7679 (mttm) REVERT: I 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: J 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7340 (ttpp) REVERT: J 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7464 (tttm) REVERT: J 143 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7660 (mttp) REVERT: J 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: K 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7338 (ttpp) REVERT: K 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: K 143 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7676 (mttm) REVERT: K 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: L 53 LYS cc_start: 0.7719 (ttpp) cc_final: 0.7334 (ttpp) REVERT: L 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: L 143 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7674 (mttm) REVERT: L 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: M 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7337 (ttpp) REVERT: M 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7467 (tttm) REVERT: M 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7673 (mttm) REVERT: M 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: N 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7336 (ttpp) REVERT: N 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7465 (tttm) REVERT: N 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7673 (mttm) REVERT: N 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: O 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7337 (ttpp) REVERT: O 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7464 (tttm) REVERT: O 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7657 (mttp) REVERT: O 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: P 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7338 (ttpp) REVERT: P 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7467 (tttm) REVERT: P 143 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7679 (mttm) REVERT: P 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: Q 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7336 (ttpp) REVERT: Q 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7466 (tttm) REVERT: Q 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7679 (mttm) REVERT: Q 165 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: R 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7339 (ttpp) REVERT: R 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7464 (tttm) REVERT: R 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7657 (mttp) REVERT: R 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: S 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7335 (ttpp) REVERT: S 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: S 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7673 (mttm) REVERT: S 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: T 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7334 (ttpp) REVERT: T 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7465 (tttm) REVERT: T 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7674 (mttm) REVERT: T 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: U 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7339 (ttpp) REVERT: U 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7467 (tttm) REVERT: U 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7672 (mttm) REVERT: U 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: V 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7336 (ttpp) REVERT: V 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: V 143 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7674 (mttm) REVERT: V 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: W 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7336 (ttpp) REVERT: W 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7465 (tttm) REVERT: W 143 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7660 (mttp) REVERT: W 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: X 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7339 (ttpp) REVERT: X 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: X 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7678 (mttm) REVERT: X 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6934 (tpp) outliers start: 49 outliers final: 0 residues processed: 728 average time/residue: 1.6607 time to fit residues: 1391.4767 Evaluate side-chains 712 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 688 time to evaluate : 3.117 ------------------------------------------------------------------------------- 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: 0.9980 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 332 optimal weight: 0.9980 chunk 220 optimal weight: 0.5980 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7627 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35880 Z= 0.177 Angle : 0.547 5.061 48408 Z= 0.299 Chirality : 0.036 0.126 5016 Planarity : 0.003 0.019 6432 Dihedral : 13.331 179.620 4800 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 7.62 % 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: 5.15 (0.13), residues: 4464 helix: 3.97 (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 0.012 0.003 TRP W 93 HIS 0.012 0.002 HIS F 60 PHE 0.016 0.002 PHE D 41 TYR 0.017 0.002 TYR W 137 ARG 0.002 0.000 ARG D 90 *********************** 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 711 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 687 time to evaluate : 3.236 Fit side-chains REVERT: A 53 LYS cc_start: 0.7680 (ttpp) cc_final: 0.7283 (ttpp) REVERT: A 68 LYS cc_start: 0.7699 (ttmp) cc_final: 0.7464 (tttm) REVERT: A 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7666 (mttp) REVERT: A 165 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: B 53 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7281 (ttpp) REVERT: B 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7466 (tttm) REVERT: B 143 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7681 (mttm) REVERT: B 165 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6938 (tpp) REVERT: C 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7336 (ttpp) REVERT: C 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7465 (tttm) REVERT: C 143 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7678 (mttm) REVERT: C 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6949 (tpp) REVERT: D 53 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7285 (ttpp) REVERT: D 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7464 (tttm) REVERT: D 143 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7664 (mttp) REVERT: D 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: E 53 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7281 (ttpp) REVERT: E 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7465 (tttm) REVERT: E 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7680 (mttm) REVERT: E 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: F 53 LYS cc_start: 0.7678 (ttpp) cc_final: 0.7283 (ttpp) REVERT: F 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7468 (tttm) REVERT: F 143 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7664 (mttp) REVERT: F 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: G 53 LYS cc_start: 0.7680 (ttpp) cc_final: 0.7282 (ttpp) REVERT: G 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7464 (tttm) REVERT: G 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7681 (mttm) REVERT: G 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: H 53 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7285 (ttpp) REVERT: H 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7465 (tttm) REVERT: H 143 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7680 (mttm) REVERT: H 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: I 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7337 (ttpp) REVERT: I 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7468 (tttm) REVERT: I 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7681 (mttm) REVERT: I 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: J 53 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7285 (ttpp) REVERT: J 68 LYS cc_start: 0.7699 (ttmp) cc_final: 0.7463 (tttm) REVERT: J 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7680 (mttm) REVERT: J 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: K 53 LYS cc_start: 0.7678 (ttpp) cc_final: 0.7283 (ttpp) REVERT: K 68 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7463 (tttm) REVERT: K 143 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7668 (mttp) REVERT: K 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: L 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7336 (ttpp) REVERT: L 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7464 (tttm) REVERT: L 143 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7667 (mttp) REVERT: L 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: M 53 LYS cc_start: 0.7680 (ttpp) cc_final: 0.7284 (ttpp) REVERT: M 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7468 (tttm) REVERT: M 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7665 (mttp) REVERT: M 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: N 53 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7281 (ttpp) REVERT: N 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7465 (tttm) REVERT: N 143 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7665 (mttp) REVERT: N 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: O 53 LYS cc_start: 0.7680 (ttpp) cc_final: 0.7283 (ttpp) REVERT: O 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7465 (tttm) REVERT: O 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7683 (mttm) REVERT: O 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: P 53 LYS cc_start: 0.7678 (ttpp) cc_final: 0.7282 (ttpp) REVERT: P 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7467 (tttm) REVERT: P 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7681 (mttm) REVERT: P 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: Q 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7335 (ttpp) REVERT: Q 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7466 (tttm) REVERT: Q 143 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7682 (mttm) REVERT: Q 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: R 53 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7285 (ttpp) REVERT: R 68 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7463 (tttm) REVERT: R 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7684 (mttm) REVERT: R 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6950 (tpp) REVERT: S 53 LYS cc_start: 0.7678 (ttpp) cc_final: 0.7281 (ttpp) REVERT: S 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7464 (tttm) REVERT: S 143 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7665 (mttp) REVERT: S 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: T 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7335 (ttpp) REVERT: T 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7464 (tttm) REVERT: T 143 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7665 (mttp) REVERT: T 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: U 53 LYS cc_start: 0.7679 (ttpp) cc_final: 0.7283 (ttpp) REVERT: U 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7467 (tttm) REVERT: U 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7683 (mttm) REVERT: U 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: V 53 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7281 (ttpp) REVERT: V 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7464 (tttm) REVERT: V 143 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7684 (mttm) REVERT: V 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: W 53 LYS cc_start: 0.7680 (ttpp) cc_final: 0.7282 (ttpp) REVERT: W 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7465 (tttm) REVERT: W 143 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7682 (mttm) REVERT: W 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: X 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7338 (ttpp) REVERT: X 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7466 (tttm) REVERT: X 143 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7680 (mttm) REVERT: X 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6951 (tpp) outliers start: 24 outliers final: 0 residues processed: 687 average time/residue: 1.6972 time to fit residues: 1339.8242 Evaluate side-chains 711 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 687 time to evaluate : 3.076 ------------------------------------------------------------------------------- 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: 6.9990 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 267 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 309 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: