Starting phenix.real_space_refine on Tue Aug 26 06:51:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cu8_26996/08_2025/8cu8_26996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cu8_26996/08_2025/8cu8_26996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cu8_26996/08_2025/8cu8_26996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cu8_26996/08_2025/8cu8_26996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cu8_26996/08_2025/8cu8_26996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cu8_26996/08_2025/8cu8_26996.map" } resolution = 1.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 72 5.16 5 C 20784 2.51 5 N 5688 2.21 5 O 8703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35271 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "C" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "D" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "E" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "F" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "G" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "H" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "I" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "J" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "K" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "L" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "M" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "N" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "O" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "P" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "Q" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "R" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "S" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "T" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "U" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "V" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "W" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "X" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "Y" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 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: "C" 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: "E" 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: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" 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: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" 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: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Y" 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: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "G" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "H" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "I" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "J" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "L" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "M" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "O" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "P" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "Q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "R" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "S" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "T" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "W" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "Y" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AASN A 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 106 " occ=0.50 residue: pdb=" N AASN C 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 106 " occ=0.50 residue: pdb=" N AASN D 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D 106 " occ=0.50 residue: pdb=" N AASN E 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN E 106 " occ=0.50 residue: pdb=" N AASN F 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN F 106 " occ=0.50 residue: pdb=" N AASN G 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN G 106 " occ=0.50 residue: pdb=" N AASN H 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN H 106 " occ=0.50 residue: pdb=" N AASN I 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN I 106 " occ=0.50 residue: pdb=" N AASN J 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN J 106 " occ=0.50 residue: pdb=" N AASN K 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN K 106 " occ=0.50 residue: pdb=" N AASN L 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN L 106 " occ=0.50 residue: pdb=" N AASN M 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN M 106 " occ=0.50 ... (remaining 36 not shown) Time building chain proxies: 14.43, per 1000 atoms: 0.41 Number of scatterers: 35271 At special positions: 0 Unit cell: (128.74, 128.74, 128.74, 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 24 26.01 S 72 16.00 O 8703 8.00 N 5688 7.00 C 20784 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: 2.49 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7776 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 9 through 37 Processing helix chain 'A' and resid 44 through 72 Processing helix chain 'A' and resid 91 through 120 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 155 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'C' and resid 9 through 37 Processing helix chain 'C' and resid 44 through 72 Processing helix chain 'C' and resid 91 through 120 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 155 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'D' and resid 9 through 37 Processing helix chain 'D' and resid 44 through 72 Processing helix chain 'D' and resid 91 through 120 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 133 through 155 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'E' and resid 9 through 37 Processing helix chain 'E' and resid 44 through 72 Processing helix chain 'E' and resid 91 through 120 Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 133 through 155 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'F' and resid 9 through 37 Processing helix chain 'F' and resid 44 through 72 Processing helix chain 'F' and resid 91 through 120 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 155 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'G' and resid 9 through 37 Processing helix chain 'G' and resid 44 through 72 Processing helix chain 'G' and resid 91 through 120 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 133 through 155 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'H' and resid 9 through 37 Processing helix chain 'H' and resid 44 through 72 Processing helix chain 'H' and resid 91 through 120 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 133 through 155 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'I' and resid 9 through 37 Processing helix chain 'I' and resid 44 through 72 Processing helix chain 'I' and resid 91 through 120 Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 155 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'J' and resid 9 through 37 Processing helix chain 'J' and resid 44 through 72 Processing helix chain 'J' and resid 91 through 120 Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 133 through 155 Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'K' and resid 9 through 37 Processing helix chain 'K' and resid 44 through 72 Processing helix chain 'K' and resid 91 through 120 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 133 through 155 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'L' and resid 9 through 37 Processing helix chain 'L' and resid 44 through 72 Processing helix chain 'L' and resid 91 through 120 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 133 through 155 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'M' and resid 9 through 37 Processing helix chain 'M' and resid 44 through 72 Processing helix chain 'M' and resid 91 through 120 Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 133 through 155 Processing helix chain 'M' and resid 157 through 167 Processing helix chain 'N' and resid 9 through 37 Processing helix chain 'N' and resid 44 through 72 Processing helix chain 'N' and resid 91 through 120 Processing helix chain 'N' and resid 122 through 133 Processing helix chain 'N' and resid 133 through 155 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'O' and resid 9 through 37 Processing helix chain 'O' and resid 44 through 72 Processing helix chain 'O' and resid 91 through 120 Processing helix chain 'O' and resid 122 through 133 Processing helix chain 'O' and resid 133 through 155 Processing helix chain 'O' and resid 157 through 167 Processing helix chain 'P' and resid 9 through 37 Processing helix chain 'P' and resid 44 through 72 Processing helix chain 'P' and resid 91 through 120 Processing helix chain 'P' and resid 122 through 133 Processing helix chain 'P' and resid 133 through 155 Processing helix chain 'P' and resid 157 through 167 Processing helix chain 'Q' and resid 9 through 37 Processing helix chain 'Q' and resid 44 through 72 Processing helix chain 'Q' and resid 91 through 120 Processing helix chain 'Q' and resid 122 through 133 Processing helix chain 'Q' and resid 133 through 155 Processing helix chain 'Q' and resid 157 through 167 Processing helix chain 'R' and resid 9 through 37 Processing helix chain 'R' and resid 44 through 72 Processing helix chain 'R' and resid 91 through 120 Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 133 through 155 Processing helix chain 'R' and resid 157 through 167 Processing helix chain 'S' and resid 9 through 37 Processing helix chain 'S' and resid 44 through 72 Processing helix chain 'S' and resid 91 through 120 Processing helix chain 'S' and resid 122 through 133 Processing helix chain 'S' and resid 133 through 155 Processing helix chain 'S' and resid 157 through 167 Processing helix chain 'T' and resid 9 through 37 Processing helix chain 'T' and resid 44 through 72 Processing helix chain 'T' and resid 91 through 120 Processing helix chain 'T' and resid 122 through 133 Processing helix chain 'T' and resid 133 through 155 Processing helix chain 'T' and resid 157 through 167 Processing helix chain 'U' and resid 9 through 37 Processing helix chain 'U' and resid 44 through 72 Processing helix chain 'U' and resid 91 through 120 Processing helix chain 'U' and resid 122 through 133 Processing helix chain 'U' and resid 133 through 155 Processing helix chain 'U' and resid 157 through 167 Processing helix chain 'V' and resid 9 through 37 Processing helix chain 'V' and resid 44 through 72 Processing helix chain 'V' and resid 91 through 120 Processing helix chain 'V' and resid 122 through 133 Processing helix chain 'V' and resid 133 through 155 Processing helix chain 'V' and resid 157 through 167 Processing helix chain 'W' and resid 9 through 37 Processing helix chain 'W' and resid 44 through 72 Processing helix chain 'W' and resid 91 through 120 Processing helix chain 'W' and resid 122 through 133 Processing helix chain 'W' and resid 133 through 155 Processing helix chain 'W' and resid 157 through 167 Processing helix chain 'X' and resid 9 through 37 Processing helix chain 'X' and resid 44 through 72 Processing helix chain 'X' and resid 91 through 120 Processing helix chain 'X' and resid 122 through 133 Processing helix chain 'X' and resid 133 through 155 Processing helix chain 'X' and resid 157 through 167 Processing helix chain 'Y' and resid 9 through 37 Processing helix chain 'Y' and resid 44 through 72 Processing helix chain 'Y' and resid 91 through 120 Processing helix chain 'Y' and resid 122 through 133 Processing helix chain 'Y' and resid 133 through 155 Processing helix chain 'Y' and resid 157 through 167 2688 hydrogen bonds defined for protein. 8088 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: 6.06 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10156 1.34 - 1.45: 5035 1.45 - 1.57: 18313 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 33648 Sorted by residual: bond pdb=" C GLY W 157 " pdb=" O GLY W 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 bond pdb=" C GLY D 157 " pdb=" O GLY D 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 bond pdb=" C GLY C 157 " pdb=" O GLY C 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 bond pdb=" C GLY F 157 " pdb=" O GLY F 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 bond pdb=" C GLY H 157 " pdb=" O GLY H 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 ... (remaining 33643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 43938 1.51 - 3.01: 1256 3.01 - 4.52: 138 4.52 - 6.02: 52 6.02 - 7.53: 24 Bond angle restraints: 45408 Sorted by residual: angle pdb=" C SER E 34 " pdb=" N PHE E 35 " pdb=" CA PHE E 35 " ideal model delta sigma weight residual 122.06 116.42 5.64 1.86e+00 2.89e-01 9.18e+00 angle pdb=" C SER H 34 " pdb=" N PHE H 35 " pdb=" CA PHE H 35 " ideal model delta sigma weight residual 122.06 116.43 5.63 1.86e+00 2.89e-01 9.18e+00 angle pdb=" C SER Y 34 " pdb=" N PHE Y 35 " pdb=" CA PHE Y 35 " ideal model delta sigma weight residual 122.06 116.44 5.62 1.86e+00 2.89e-01 9.13e+00 angle pdb=" C SER C 34 " pdb=" N PHE C 35 " pdb=" CA PHE C 35 " ideal model delta sigma weight residual 122.06 116.46 5.60 1.86e+00 2.89e-01 9.06e+00 angle pdb=" C SER W 34 " pdb=" N PHE W 35 " pdb=" CA PHE W 35 " ideal model delta sigma weight residual 122.06 116.46 5.60 1.86e+00 2.89e-01 9.06e+00 ... (remaining 45403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 18204 16.69 - 33.37: 1605 33.37 - 50.06: 331 50.06 - 66.75: 68 66.75 - 83.44: 48 Dihedral angle restraints: 20256 sinusoidal: 8256 harmonic: 12000 Sorted by residual: dihedral pdb=" CA VAL S 42 " pdb=" C VAL S 42 " pdb=" N ALA S 43 " pdb=" CA ALA S 43 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA VAL O 42 " pdb=" C VAL O 42 " pdb=" N ALA O 43 " pdb=" CA ALA O 43 " ideal model delta harmonic sigma weight residual 180.00 163.98 16.02 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA VAL J 42 " pdb=" C VAL J 42 " pdb=" N ALA J 43 " pdb=" CA ALA J 43 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 20253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2801 0.033 - 0.066: 1228 0.066 - 0.099: 527 0.099 - 0.132: 168 0.132 - 0.165: 76 Chirality restraints: 4800 Sorted by residual: chirality pdb=" CA PHE N 35 " pdb=" N PHE N 35 " pdb=" C PHE N 35 " pdb=" CB PHE N 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA PHE T 35 " pdb=" N PHE T 35 " pdb=" C PHE T 35 " pdb=" CB PHE T 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 4797 not shown) Planarity restraints: 6072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 28 " -0.036 2.00e-02 2.50e+03 2.91e-02 1.69e+01 pdb=" CG TYR Q 28 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 28 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 28 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 28 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR Q 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR Q 28 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 28 " 0.036 2.00e-02 2.50e+03 2.90e-02 1.69e+01 pdb=" CG TYR F 28 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR F 28 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR F 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR F 28 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR F 28 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 28 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 28 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 28 " -0.036 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR T 28 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR T 28 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR T 28 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR T 28 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR T 28 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR T 28 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR T 28 " -0.005 2.00e-02 2.50e+03 ... (remaining 6069 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 535 2.61 - 3.19: 30507 3.19 - 3.76: 58587 3.76 - 4.33: 86796 4.33 - 4.90: 133849 Nonbonded interactions: 310274 Sorted by model distance: nonbonded pdb="FE FE A 201 " pdb=" O HOH A 360 " model vdw 2.043 2.260 nonbonded pdb="FE FE F 201 " pdb=" O HOH F 359 " model vdw 2.043 2.260 nonbonded pdb="FE FE U 201 " pdb=" O HOH U 359 " model vdw 2.043 2.260 nonbonded pdb="FE FE V 201 " pdb=" O HOH V 359 " model vdw 2.043 2.260 nonbonded pdb="FE FE I 201 " pdb=" O HOH I 359 " model vdw 2.043 2.260 ... (remaining 310269 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'C' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'D' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'E' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'F' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'G' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'H' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'I' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'J' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'K' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'L' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'M' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'N' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'O' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'P' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'Q' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'R' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'S' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'T' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'U' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'V' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'W' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'X' and (resid 2 through 105 or resid 107 through 201)) selection = (chain 'Y' and (resid 2 through 105 or resid 107 through 201)) } 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=0.50 max=1.00 mean=0.99 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 35.830 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 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 : 0.005 0.034 33648 Z= 0.268 Angle : 0.650 7.527 45408 Z= 0.398 Chirality : 0.048 0.165 4800 Planarity : 0.005 0.040 6072 Dihedral : 13.913 83.436 12480 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.11), residues: 4056 helix: 1.29 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : -0.89 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.071 0.004 TYR Q 28 PHE 0.023 0.003 PHE H 35 TRP 0.005 0.001 TRP I 89 HIS 0.004 0.001 HIS V 114 Details of bonding type rmsd covalent geometry : bond 0.00526 (33648) covalent geometry : angle 0.64951 (45408) hydrogen bonds : bond 0.14810 ( 2688) hydrogen bonds : angle 3.72622 ( 8088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 720 time to evaluate : 1.236 Fit side-chains REVERT: A 147 MET cc_start: 0.9134 (mtm) cc_final: 0.8859 (mtt) REVERT: C 147 MET cc_start: 0.9132 (mtm) cc_final: 0.8858 (mtt) REVERT: D 147 MET cc_start: 0.9135 (mtm) cc_final: 0.8860 (mtt) REVERT: E 147 MET cc_start: 0.9134 (mtm) cc_final: 0.8863 (mtt) REVERT: F 147 MET cc_start: 0.9136 (mtm) cc_final: 0.8860 (mtt) REVERT: G 147 MET cc_start: 0.9140 (mtm) cc_final: 0.8866 (mtt) REVERT: H 147 MET cc_start: 0.9135 (mtm) cc_final: 0.8861 (mtt) REVERT: I 147 MET cc_start: 0.9134 (mtm) cc_final: 0.8859 (mtt) REVERT: J 147 MET cc_start: 0.9141 (mtm) cc_final: 0.8871 (mtt) REVERT: K 147 MET cc_start: 0.9138 (mtm) cc_final: 0.8863 (mtt) REVERT: L 147 MET cc_start: 0.9141 (mtm) cc_final: 0.8868 (mtt) REVERT: M 147 MET cc_start: 0.9133 (mtm) cc_final: 0.8860 (mtt) REVERT: N 147 MET cc_start: 0.9144 (mtm) cc_final: 0.8869 (mtt) REVERT: O 147 MET cc_start: 0.9137 (mtm) cc_final: 0.8862 (mtt) REVERT: P 147 MET cc_start: 0.9141 (mtm) cc_final: 0.8867 (mtt) REVERT: Q 147 MET cc_start: 0.9137 (mtm) cc_final: 0.8863 (mtt) REVERT: R 147 MET cc_start: 0.9139 (mtm) cc_final: 0.8865 (mtt) REVERT: S 147 MET cc_start: 0.9139 (mtm) cc_final: 0.8864 (mtt) REVERT: T 147 MET cc_start: 0.9136 (mtm) cc_final: 0.8862 (mtt) REVERT: U 147 MET cc_start: 0.9133 (mtm) cc_final: 0.8861 (mtt) REVERT: V 147 MET cc_start: 0.9139 (mtm) cc_final: 0.8863 (mtt) REVERT: W 147 MET cc_start: 0.9134 (mtm) cc_final: 0.8862 (mtt) REVERT: X 147 MET cc_start: 0.9135 (mtm) cc_final: 0.8857 (mtt) REVERT: Y 147 MET cc_start: 0.9142 (mtm) cc_final: 0.8870 (mtt) outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 0.8459 time to fit residues: 698.9548 Evaluate side-chains 574 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 574 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 167 HIS C 79 GLN C 167 HIS D 79 GLN D 82 GLN D 142 ASN D 167 HIS E 79 GLN E 82 GLN E 167 HIS F 79 GLN F 82 GLN F 167 HIS G 79 GLN G 82 GLN G 167 HIS H 79 GLN H 82 GLN H 167 HIS I 79 GLN I 167 HIS J 79 GLN J 82 GLN J 142 ASN J 167 HIS K 79 GLN K 82 GLN K 167 HIS L 79 GLN L 167 HIS M 79 GLN M 167 HIS N 79 GLN N 82 GLN N 167 HIS O 79 GLN O 82 GLN O 142 ASN O 167 HIS P 79 GLN P 82 GLN P 167 HIS Q 79 GLN Q 142 ASN Q 167 HIS R 79 GLN R 82 GLN R 142 ASN R 167 HIS S 79 GLN S 82 GLN S 142 ASN S 167 HIS T 79 GLN T 82 GLN T 167 HIS U 79 GLN U 82 GLN U 142 ASN U 167 HIS V 79 GLN V 82 GLN V 142 ASN V 167 HIS W 79 GLN W 82 GLN W 142 ASN W 167 HIS X 79 GLN X 82 GLN X 167 HIS Y 79 GLN Y 142 ASN Y 167 HIS Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.086294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.070744 restraints weight = 182152.633| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.18 r_work: 0.2557 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33648 Z= 0.138 Angle : 0.483 6.854 45408 Z= 0.264 Chirality : 0.038 0.135 4800 Planarity : 0.003 0.031 6072 Dihedral : 4.144 14.997 4416 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.41 (0.13), residues: 4056 helix: 3.53 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.43 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 75 TYR 0.032 0.002 TYR F 28 PHE 0.016 0.002 PHE O 35 TRP 0.005 0.001 TRP E 89 HIS 0.002 0.001 HIS G 120 Details of bonding type rmsd covalent geometry : bond 0.00258 (33648) covalent geometry : angle 0.48292 (45408) hydrogen bonds : bond 0.07546 ( 2688) hydrogen bonds : angle 3.38763 ( 8088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 1.304 Fit side-chains REVERT: A 147 MET cc_start: 0.9393 (mtm) cc_final: 0.9149 (mtt) REVERT: C 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9151 (mtt) REVERT: D 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9150 (mtt) REVERT: E 147 MET cc_start: 0.9397 (mtm) cc_final: 0.9155 (mtt) REVERT: F 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9150 (mtt) REVERT: G 147 MET cc_start: 0.9392 (mtm) cc_final: 0.9155 (mtt) REVERT: H 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9151 (mtt) REVERT: I 147 MET cc_start: 0.9392 (mtm) cc_final: 0.9148 (mtt) REVERT: J 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9164 (mtt) REVERT: K 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9151 (mtt) REVERT: L 147 MET cc_start: 0.9396 (mtm) cc_final: 0.9160 (mtt) REVERT: M 147 MET cc_start: 0.9391 (mtm) cc_final: 0.9149 (mtt) REVERT: N 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9157 (mtt) REVERT: O 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9152 (mtt) REVERT: P 147 MET cc_start: 0.9393 (mtm) cc_final: 0.9156 (mtt) REVERT: Q 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9152 (mtt) REVERT: R 147 MET cc_start: 0.9392 (mtm) cc_final: 0.9156 (mtt) REVERT: S 147 MET cc_start: 0.9391 (mtm) cc_final: 0.9153 (mtt) REVERT: T 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9152 (mtt) REVERT: U 147 MET cc_start: 0.9389 (mtm) cc_final: 0.9145 (mtt) REVERT: V 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9150 (mtt) REVERT: W 147 MET cc_start: 0.9391 (mtm) cc_final: 0.9149 (mtt) REVERT: X 147 MET cc_start: 0.9393 (mtm) cc_final: 0.9150 (mtt) REVERT: Y 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9159 (mtt) outliers start: 0 outliers final: 0 residues processed: 646 average time/residue: 0.7791 time to fit residues: 587.2591 Evaluate side-chains 571 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 291 optimal weight: 6.9990 chunk 350 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 chunk 324 optimal weight: 9.9990 chunk 373 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN N 82 GLN O 82 GLN P 82 GLN S 82 GLN T 82 GLN U 82 GLN V 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.086296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.070367 restraints weight = 194385.161| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.33 r_work: 0.2570 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 33648 Z= 0.131 Angle : 0.468 6.686 45408 Z= 0.252 Chirality : 0.037 0.129 4800 Planarity : 0.003 0.029 6072 Dihedral : 3.975 14.715 4416 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.33 (0.13), residues: 4056 helix: 4.16 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.08 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 72 TYR 0.027 0.002 TYR F 28 PHE 0.014 0.001 PHE X 35 TRP 0.005 0.001 TRP L 89 HIS 0.002 0.001 HIS J 124 Details of bonding type rmsd covalent geometry : bond 0.00240 (33648) covalent geometry : angle 0.46776 (45408) hydrogen bonds : bond 0.06969 ( 2688) hydrogen bonds : angle 3.32280 ( 8088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 0.922 Fit side-chains REVERT: A 147 MET cc_start: 0.9393 (mtm) cc_final: 0.9152 (mtt) REVERT: C 38 ASP cc_start: 0.9027 (t0) cc_final: 0.8826 (t70) REVERT: C 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9150 (mtt) REVERT: D 147 MET cc_start: 0.9397 (mtm) cc_final: 0.9153 (mtt) REVERT: E 38 ASP cc_start: 0.9032 (t0) cc_final: 0.8828 (t70) REVERT: E 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9157 (mtt) REVERT: F 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9153 (mtt) REVERT: G 147 MET cc_start: 0.9391 (mtm) cc_final: 0.9155 (mtt) REVERT: H 147 MET cc_start: 0.9391 (mtm) cc_final: 0.9149 (mtt) REVERT: I 147 MET cc_start: 0.9399 (mtm) cc_final: 0.9156 (mtt) REVERT: J 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9162 (mtt) REVERT: K 38 ASP cc_start: 0.9034 (t0) cc_final: 0.8833 (t70) REVERT: K 147 MET cc_start: 0.9393 (mtm) cc_final: 0.9151 (mtt) REVERT: L 147 MET cc_start: 0.9396 (mtm) cc_final: 0.9160 (mtt) REVERT: M 147 MET cc_start: 0.9391 (mtm) cc_final: 0.9150 (mtt) REVERT: N 147 MET cc_start: 0.9389 (mtm) cc_final: 0.9153 (mtt) REVERT: O 147 MET cc_start: 0.9396 (mtm) cc_final: 0.9155 (mtt) REVERT: P 147 MET cc_start: 0.9390 (mtm) cc_final: 0.9156 (mtt) REVERT: Q 147 MET cc_start: 0.9396 (mtm) cc_final: 0.9156 (mtt) REVERT: R 147 MET cc_start: 0.9389 (mtm) cc_final: 0.9152 (mtt) REVERT: S 147 MET cc_start: 0.9392 (mtm) cc_final: 0.9155 (mtt) REVERT: T 147 MET cc_start: 0.9396 (mtm) cc_final: 0.9154 (mtt) REVERT: U 147 MET cc_start: 0.9387 (mtm) cc_final: 0.9146 (mtt) REVERT: V 38 ASP cc_start: 0.9018 (t0) cc_final: 0.8812 (t70) REVERT: V 147 MET cc_start: 0.9388 (mtm) cc_final: 0.9146 (mtt) REVERT: W 147 MET cc_start: 0.9391 (mtm) cc_final: 0.9151 (mtt) REVERT: X 147 MET cc_start: 0.9392 (mtm) cc_final: 0.9150 (mtt) REVERT: Y 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9161 (mtt) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.7723 time to fit residues: 497.6827 Evaluate side-chains 494 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 187 optimal weight: 0.9990 chunk 316 optimal weight: 1.9990 chunk 361 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 365 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN L 82 GLN M 82 GLN N 82 GLN O 82 GLN P 82 GLN Q 82 GLN S 82 GLN T 82 GLN U 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.082797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.066778 restraints weight = 184755.980| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.30 r_work: 0.2496 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9202 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 33648 Z= 0.160 Angle : 0.495 6.322 45408 Z= 0.271 Chirality : 0.039 0.140 4800 Planarity : 0.003 0.028 6072 Dihedral : 4.019 14.189 4416 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.20 % Allowed : 9.05 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.38 (0.13), residues: 4056 helix: 4.19 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.02 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 72 TYR 0.031 0.002 TYR F 28 PHE 0.016 0.002 PHE H 35 TRP 0.005 0.001 TRP J 89 HIS 0.002 0.001 HIS L 114 Details of bonding type rmsd covalent geometry : bond 0.00320 (33648) covalent geometry : angle 0.49477 (45408) hydrogen bonds : bond 0.08370 ( 2688) hydrogen bonds : angle 3.54265 ( 8088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 486 time to evaluate : 1.416 Fit side-chains REVERT: A 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9169 (mtt) REVERT: C 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9176 (mtt) REVERT: D 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9170 (mtt) REVERT: E 147 MET cc_start: 0.9411 (mtm) cc_final: 0.9172 (mtt) REVERT: F 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9168 (mtt) REVERT: G 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9159 (mtt) REVERT: H 147 MET cc_start: 0.9411 (mtm) cc_final: 0.9173 (mtt) REVERT: I 147 MET cc_start: 0.9412 (mtm) cc_final: 0.9172 (mtt) REVERT: J 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9168 (mtt) REVERT: K 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9171 (mtt) REVERT: L 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9160 (mtt) REVERT: M 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9172 (mtt) REVERT: N 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9158 (mtt) REVERT: O 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9171 (mtt) REVERT: P 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9158 (mtt) REVERT: Q 147 MET cc_start: 0.9412 (mtm) cc_final: 0.9173 (mtt) REVERT: R 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9158 (mtt) REVERT: S 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9156 (mtt) REVERT: T 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9168 (mtt) REVERT: U 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9163 (mtt) REVERT: V 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9173 (mtt) REVERT: W 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9174 (mtt) REVERT: X 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9168 (mtt) REVERT: Y 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9161 (mtt) outliers start: 7 outliers final: 0 residues processed: 486 average time/residue: 0.7300 time to fit residues: 415.0551 Evaluate side-chains 462 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 374 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 315 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 356 optimal weight: 0.7980 chunk 321 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN N 82 GLN O 82 GLN P 82 GLN R 82 GLN S 82 GLN T 82 GLN U 82 GLN V 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.086376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.070245 restraints weight = 193746.628| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.36 r_work: 0.2566 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 33648 Z= 0.128 Angle : 0.457 6.509 45408 Z= 0.248 Chirality : 0.038 0.130 4800 Planarity : 0.002 0.027 6072 Dihedral : 3.919 14.376 4416 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.66 (0.13), residues: 4056 helix: 4.37 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.17 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 72 TYR 0.019 0.002 TYR F 28 PHE 0.014 0.002 PHE H 35 TRP 0.005 0.001 TRP H 89 HIS 0.001 0.001 HIS F 167 Details of bonding type rmsd covalent geometry : bond 0.00234 (33648) covalent geometry : angle 0.45718 (45408) hydrogen bonds : bond 0.06783 ( 2688) hydrogen bonds : angle 3.34350 ( 8088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.399 Fit side-chains REVERT: A 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9146 (mtt) REVERT: C 131 GLU cc_start: 0.8475 (tp30) cc_final: 0.8129 (tp30) REVERT: C 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9146 (mtt) REVERT: D 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9149 (mtt) REVERT: E 131 GLU cc_start: 0.8461 (tp30) cc_final: 0.8114 (tp30) REVERT: E 147 MET cc_start: 0.9400 (mtm) cc_final: 0.9152 (mtt) REVERT: F 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9146 (mtt) REVERT: G 147 MET cc_start: 0.9389 (mtm) cc_final: 0.9147 (mtt) REVERT: H 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9148 (mtt) REVERT: I 131 GLU cc_start: 0.8496 (tp30) cc_final: 0.8145 (tp30) REVERT: I 147 MET cc_start: 0.9397 (mtm) cc_final: 0.9150 (mtt) REVERT: J 147 MET cc_start: 0.9400 (mtm) cc_final: 0.9157 (mtt) REVERT: K 131 GLU cc_start: 0.8499 (tp30) cc_final: 0.8149 (tp30) REVERT: K 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9148 (mtt) REVERT: L 147 MET cc_start: 0.9391 (mtm) cc_final: 0.9147 (mtt) REVERT: M 131 GLU cc_start: 0.8469 (tp30) cc_final: 0.8132 (tp30) REVERT: M 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9153 (mtt) REVERT: N 147 MET cc_start: 0.9385 (mtm) cc_final: 0.9142 (mtt) REVERT: O 131 GLU cc_start: 0.8483 (tp30) cc_final: 0.8138 (tp30) REVERT: O 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9148 (mtt) REVERT: P 147 MET cc_start: 0.9392 (mtm) cc_final: 0.9148 (mtt) REVERT: Q 131 GLU cc_start: 0.8504 (tp30) cc_final: 0.8153 (tp30) REVERT: Q 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9148 (mtt) REVERT: R 147 MET cc_start: 0.9386 (mtm) cc_final: 0.9143 (mtt) REVERT: S 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9150 (mtt) REVERT: T 147 MET cc_start: 0.9396 (mtm) cc_final: 0.9149 (mtt) REVERT: U 147 MET cc_start: 0.9392 (mtm) cc_final: 0.9145 (mtt) REVERT: V 147 MET cc_start: 0.9393 (mtm) cc_final: 0.9173 (mtt) REVERT: W 147 MET cc_start: 0.9393 (mtm) cc_final: 0.9176 (mtt) REVERT: X 147 MET cc_start: 0.9396 (mtm) cc_final: 0.9148 (mtt) REVERT: Y 147 MET cc_start: 0.9396 (mtm) cc_final: 0.9155 (mtt) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.7373 time to fit residues: 419.6206 Evaluate side-chains 466 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 172 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 378 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 293 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN L 82 GLN N 82 GLN O 82 GLN P 82 GLN Q 82 GLN S 82 GLN T 82 GLN U 82 GLN V 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.083529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.067412 restraints weight = 185436.595| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.32 r_work: 0.2508 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33648 Z= 0.151 Angle : 0.480 6.299 45408 Z= 0.264 Chirality : 0.039 0.138 4800 Planarity : 0.003 0.028 6072 Dihedral : 3.962 13.944 4416 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.58 (0.13), residues: 4056 helix: 4.29 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : 0.24 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 72 TYR 0.024 0.002 TYR J 28 PHE 0.016 0.002 PHE M 35 TRP 0.004 0.001 TRP J 89 HIS 0.002 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00297 (33648) covalent geometry : angle 0.48019 (45408) hydrogen bonds : bond 0.07981 ( 2688) hydrogen bonds : angle 3.51028 ( 8088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.026 Fit side-chains REVERT: A 147 MET cc_start: 0.9396 (mtm) cc_final: 0.9154 (mtt) REVERT: C 131 GLU cc_start: 0.8499 (tp30) cc_final: 0.8077 (tp30) REVERT: C 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9166 (mtt) REVERT: D 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9160 (mtt) REVERT: E 131 GLU cc_start: 0.8488 (tp30) cc_final: 0.8069 (tp30) REVERT: E 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9165 (mtt) REVERT: F 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9162 (mtt) REVERT: G 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9169 (mtt) REVERT: H 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9163 (mtt) REVERT: I 131 GLU cc_start: 0.8468 (tp30) cc_final: 0.8135 (tp30) REVERT: I 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9164 (mtt) REVERT: J 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9174 (mtt) REVERT: K 131 GLU cc_start: 0.8482 (tp30) cc_final: 0.8146 (tp30) REVERT: K 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9163 (mtt) REVERT: L 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9168 (mtt) REVERT: M 131 GLU cc_start: 0.8483 (tp30) cc_final: 0.8068 (tp30) REVERT: M 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9164 (mtt) REVERT: N 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9168 (mtt) REVERT: O 131 GLU cc_start: 0.8461 (tp30) cc_final: 0.8131 (tp30) REVERT: O 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9163 (mtt) REVERT: P 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9167 (mtt) REVERT: Q 131 GLU cc_start: 0.8473 (tp30) cc_final: 0.8138 (tp30) REVERT: Q 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9164 (mtt) REVERT: R 147 MET cc_start: 0.9399 (mtm) cc_final: 0.9165 (mtt) REVERT: S 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9166 (mtt) REVERT: T 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9162 (mtt) REVERT: U 147 MET cc_start: 0.9399 (mtm) cc_final: 0.9157 (mtt) REVERT: V 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9159 (mtt) REVERT: W 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9161 (mtt) REVERT: X 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9164 (mtt) REVERT: Y 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9172 (mtt) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.7721 time to fit residues: 439.2927 Evaluate side-chains 486 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 195 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 353 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 281 optimal weight: 2.9990 chunk 360 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN L 82 GLN N 82 GLN O 82 GLN P 82 GLN Q 82 GLN S 82 GLN T 82 GLN U 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.082117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.065911 restraints weight = 195027.958| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.38 r_work: 0.2472 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9215 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 33648 Z= 0.170 Angle : 0.499 6.284 45408 Z= 0.277 Chirality : 0.040 0.143 4800 Planarity : 0.003 0.027 6072 Dihedral : 4.018 14.208 4416 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.45 (0.13), residues: 4056 helix: 4.20 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : 0.19 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 72 TYR 0.026 0.002 TYR Q 28 PHE 0.016 0.002 PHE D 35 TRP 0.005 0.001 TRP U 89 HIS 0.003 0.001 HIS F 114 Details of bonding type rmsd covalent geometry : bond 0.00350 (33648) covalent geometry : angle 0.49901 (45408) hydrogen bonds : bond 0.08715 ( 2688) hydrogen bonds : angle 3.61239 ( 8088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 1.186 Fit side-chains REVERT: A 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9165 (mtt) REVERT: C 131 GLU cc_start: 0.8519 (tp30) cc_final: 0.8103 (tp30) REVERT: C 147 MET cc_start: 0.9422 (mtm) cc_final: 0.9171 (mtt) REVERT: D 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9163 (mtt) REVERT: E 131 GLU cc_start: 0.8509 (tp30) cc_final: 0.8093 (tp30) REVERT: E 147 MET cc_start: 0.9423 (mtm) cc_final: 0.9172 (mtt) REVERT: F 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9165 (mtt) REVERT: G 147 MET cc_start: 0.9418 (mtm) cc_final: 0.9173 (mtt) REVERT: H 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9167 (mtt) REVERT: I 131 GLU cc_start: 0.8474 (tp30) cc_final: 0.8142 (tp30) REVERT: I 147 MET cc_start: 0.9419 (mtm) cc_final: 0.9168 (mtt) REVERT: J 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9171 (mtt) REVERT: K 131 GLU cc_start: 0.8479 (tp30) cc_final: 0.8145 (tp30) REVERT: K 147 MET cc_start: 0.9419 (mtm) cc_final: 0.9171 (mtt) REVERT: L 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9169 (mtt) REVERT: M 131 GLU cc_start: 0.8499 (tp30) cc_final: 0.8088 (tp30) REVERT: M 147 MET cc_start: 0.9419 (mtm) cc_final: 0.9170 (mtt) REVERT: N 147 MET cc_start: 0.9413 (mtm) cc_final: 0.9168 (mtt) REVERT: O 131 GLU cc_start: 0.8463 (tp30) cc_final: 0.8132 (tp30) REVERT: O 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9166 (mtt) REVERT: P 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9170 (mtt) REVERT: Q 131 GLU cc_start: 0.8478 (tp30) cc_final: 0.8142 (tp30) REVERT: Q 147 MET cc_start: 0.9419 (mtm) cc_final: 0.9169 (mtt) REVERT: R 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9169 (mtt) REVERT: S 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9166 (mtt) REVERT: T 147 MET cc_start: 0.9413 (mtm) cc_final: 0.9163 (mtt) REVERT: U 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9164 (mtt) REVERT: V 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9170 (mtt) REVERT: W 147 MET cc_start: 0.9418 (mtm) cc_final: 0.9169 (mtt) REVERT: X 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9168 (mtt) REVERT: Y 147 MET cc_start: 0.9416 (mtm) cc_final: 0.9170 (mtt) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.7771 time to fit residues: 416.8212 Evaluate side-chains 461 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 2 optimal weight: 7.9990 chunk 359 optimal weight: 4.9990 chunk 351 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 322 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 368 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN N 82 GLN O 82 GLN P 82 GLN S 82 GLN T 82 GLN U 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.085241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.069117 restraints weight = 187875.178| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.32 r_work: 0.2545 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33648 Z= 0.135 Angle : 0.462 6.444 45408 Z= 0.253 Chirality : 0.038 0.133 4800 Planarity : 0.002 0.027 6072 Dihedral : 3.936 14.098 4416 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.72 (0.13), residues: 4056 helix: 4.38 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : 0.33 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 72 TYR 0.018 0.002 TYR J 28 PHE 0.015 0.002 PHE Y 35 TRP 0.005 0.001 TRP U 89 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00250 (33648) covalent geometry : angle 0.46239 (45408) hydrogen bonds : bond 0.07152 ( 2688) hydrogen bonds : angle 3.40833 ( 8088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.216 Fit side-chains REVERT: A 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9162 (mtt) REVERT: C 131 GLU cc_start: 0.8510 (tp30) cc_final: 0.8101 (tp30) REVERT: C 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9168 (mtt) REVERT: D 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9168 (mtt) REVERT: E 131 GLU cc_start: 0.8485 (tp30) cc_final: 0.8076 (tp30) REVERT: E 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9163 (mtt) REVERT: F 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9165 (mtt) REVERT: G 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9177 (mtt) REVERT: H 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9165 (mtt) REVERT: I 131 GLU cc_start: 0.8475 (tp30) cc_final: 0.8141 (tp30) REVERT: I 147 MET cc_start: 0.9411 (mtm) cc_final: 0.9170 (mtt) REVERT: J 147 MET cc_start: 0.9416 (mtm) cc_final: 0.9181 (mtt) REVERT: K 131 GLU cc_start: 0.8483 (tp30) cc_final: 0.8145 (tp30) REVERT: K 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9170 (mtt) REVERT: L 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9177 (mtt) REVERT: M 131 GLU cc_start: 0.8488 (tp30) cc_final: 0.8087 (tp30) REVERT: M 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9171 (mtt) REVERT: N 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9171 (mtt) REVERT: O 131 GLU cc_start: 0.8463 (tp30) cc_final: 0.8131 (tp30) REVERT: O 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9168 (mtt) REVERT: P 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9164 (mtt) REVERT: Q 131 GLU cc_start: 0.8480 (tp30) cc_final: 0.8143 (tp30) REVERT: Q 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9170 (mtt) REVERT: R 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9170 (mtt) REVERT: S 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9175 (mtt) REVERT: T 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9169 (mtt) REVERT: U 147 MET cc_start: 0.9397 (mtm) cc_final: 0.9156 (mtt) REVERT: V 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9168 (mtt) REVERT: W 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9161 (mtt) REVERT: X 147 MET cc_start: 0.9411 (mtm) cc_final: 0.9172 (mtt) REVERT: Y 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9182 (mtt) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.7464 time to fit residues: 424.8120 Evaluate side-chains 485 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 363 optimal weight: 7.9990 chunk 357 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 331 optimal weight: 8.9990 chunk 256 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN L 82 GLN N 82 GLN O 82 GLN P 82 GLN Q 82 GLN S 82 GLN T 82 GLN U 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.082569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.066416 restraints weight = 186986.732| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.33 r_work: 0.2484 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 33648 Z= 0.164 Angle : 0.492 6.234 45408 Z= 0.272 Chirality : 0.040 0.142 4800 Planarity : 0.003 0.028 6072 Dihedral : 3.995 14.077 4416 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.52 (0.13), residues: 4056 helix: 4.24 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : 0.29 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 72 TYR 0.025 0.002 TYR F 28 PHE 0.017 0.002 PHE F 35 TRP 0.004 0.001 TRP T 89 HIS 0.003 0.001 HIS L 124 Details of bonding type rmsd covalent geometry : bond 0.00335 (33648) covalent geometry : angle 0.49249 (45408) hydrogen bonds : bond 0.08452 ( 2688) hydrogen bonds : angle 3.57377 ( 8088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.426 Fit side-chains REVERT: A 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9168 (mtt) REVERT: C 131 GLU cc_start: 0.8509 (tp30) cc_final: 0.8099 (tp30) REVERT: C 147 MET cc_start: 0.9418 (mtm) cc_final: 0.9179 (mtt) REVERT: D 147 MET cc_start: 0.9411 (mtm) cc_final: 0.9172 (mtt) REVERT: E 131 GLU cc_start: 0.8496 (tp30) cc_final: 0.8086 (tp30) REVERT: E 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9178 (mtt) REVERT: F 147 MET cc_start: 0.9413 (mtm) cc_final: 0.9174 (mtt) REVERT: G 147 MET cc_start: 0.9412 (mtm) cc_final: 0.9166 (mtt) REVERT: H 147 MET cc_start: 0.9412 (mtm) cc_final: 0.9176 (mtt) REVERT: I 131 GLU cc_start: 0.8467 (tp30) cc_final: 0.8137 (tp30) REVERT: I 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9176 (mtt) REVERT: J 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9169 (mtt) REVERT: K 131 GLU cc_start: 0.8478 (tp30) cc_final: 0.8148 (tp30) REVERT: K 147 MET cc_start: 0.9416 (mtm) cc_final: 0.9179 (mtt) REVERT: L 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9163 (mtt) REVERT: M 131 GLU cc_start: 0.8494 (tp30) cc_final: 0.8090 (tp30) REVERT: M 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9176 (mtt) REVERT: N 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9164 (mtt) REVERT: O 131 GLU cc_start: 0.8462 (tp30) cc_final: 0.8135 (tp30) REVERT: O 147 MET cc_start: 0.9413 (mtm) cc_final: 0.9176 (mtt) REVERT: P 147 MET cc_start: 0.9413 (mtm) cc_final: 0.9164 (mtt) REVERT: Q 131 GLU cc_start: 0.8473 (tp30) cc_final: 0.8140 (tp30) REVERT: Q 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9176 (mtt) REVERT: R 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9163 (mtt) REVERT: S 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9161 (mtt) REVERT: T 147 MET cc_start: 0.9411 (mtm) cc_final: 0.9172 (mtt) REVERT: U 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9169 (mtt) REVERT: V 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9177 (mtt) REVERT: W 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9176 (mtt) REVERT: X 147 MET cc_start: 0.9413 (mtm) cc_final: 0.9175 (mtt) REVERT: Y 147 MET cc_start: 0.9412 (mtm) cc_final: 0.9166 (mtt) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.7848 time to fit residues: 421.1610 Evaluate side-chains 459 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 169 optimal weight: 9.9990 chunk 293 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 341 optimal weight: 0.6980 chunk 326 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 343 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN C 142 ASN D 82 GLN E 82 GLN E 142 ASN F 82 GLN F 142 ASN G 82 GLN G 142 ASN H 82 GLN H 142 ASN I 142 ASN J 82 GLN K 82 GLN K 142 ASN L 142 ASN M 142 ASN N 82 GLN N 142 ASN O 82 GLN P 82 GLN P 142 ASN S 82 GLN T 82 GLN T 142 ASN U 82 GLN V 82 GLN W 82 GLN X 82 GLN X 142 ASN Y 82 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.089053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.073108 restraints weight = 176536.402| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.22 r_work: 0.2612 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 33648 Z= 0.117 Angle : 0.445 6.752 45408 Z= 0.240 Chirality : 0.037 0.126 4800 Planarity : 0.002 0.026 6072 Dihedral : 3.851 14.218 4416 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.94 (0.13), residues: 4056 helix: 4.53 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.44 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 67 TYR 0.012 0.001 TYR Y 28 PHE 0.013 0.001 PHE O 35 TRP 0.006 0.001 TRP A 89 HIS 0.001 0.000 HIS F 120 Details of bonding type rmsd covalent geometry : bond 0.00207 (33648) covalent geometry : angle 0.44513 (45408) hydrogen bonds : bond 0.05808 ( 2688) hydrogen bonds : angle 3.22571 ( 8088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 1.273 Fit side-chains REVERT: A 147 MET cc_start: 0.9357 (mtm) cc_final: 0.9146 (mtt) REVERT: C 131 GLU cc_start: 0.8465 (tp30) cc_final: 0.8052 (tp30) REVERT: C 147 MET cc_start: 0.9362 (mtm) cc_final: 0.9152 (mtt) REVERT: D 147 MET cc_start: 0.9364 (mtm) cc_final: 0.9153 (mtt) REVERT: E 131 GLU cc_start: 0.8427 (tp30) cc_final: 0.8029 (tp30) REVERT: E 147 MET cc_start: 0.9362 (mtm) cc_final: 0.9152 (mtt) REVERT: F 147 MET cc_start: 0.9364 (mtm) cc_final: 0.9155 (mtt) REVERT: G 147 MET cc_start: 0.9361 (mtm) cc_final: 0.9155 (mtt) REVERT: H 147 MET cc_start: 0.9358 (mtm) cc_final: 0.9149 (mtt) REVERT: I 131 GLU cc_start: 0.8367 (tp30) cc_final: 0.8007 (tp30) REVERT: I 147 MET cc_start: 0.9365 (mtm) cc_final: 0.9157 (mtt) REVERT: J 147 MET cc_start: 0.9365 (mtm) cc_final: 0.9160 (mtt) REVERT: K 131 GLU cc_start: 0.8374 (tp30) cc_final: 0.8012 (tp30) REVERT: K 147 MET cc_start: 0.9363 (mtm) cc_final: 0.9154 (mtt) REVERT: L 147 MET cc_start: 0.9364 (mtm) cc_final: 0.9159 (mtt) REVERT: M 131 GLU cc_start: 0.8441 (tp30) cc_final: 0.8035 (tp30) REVERT: M 147 MET cc_start: 0.9363 (mtm) cc_final: 0.9155 (mtt) REVERT: N 147 MET cc_start: 0.9358 (mtm) cc_final: 0.9151 (mtt) REVERT: O 131 GLU cc_start: 0.8375 (tp30) cc_final: 0.8018 (tp30) REVERT: O 147 MET cc_start: 0.9364 (mtm) cc_final: 0.9153 (mtt) REVERT: P 147 MET cc_start: 0.9362 (mtm) cc_final: 0.9154 (mtt) REVERT: Q 131 GLU cc_start: 0.8381 (tp30) cc_final: 0.8020 (tp30) REVERT: Q 147 MET cc_start: 0.9366 (mtm) cc_final: 0.9157 (mtt) REVERT: R 147 MET cc_start: 0.9355 (mtm) cc_final: 0.9150 (mtt) REVERT: S 147 MET cc_start: 0.9362 (mtm) cc_final: 0.9155 (mtt) REVERT: T 147 MET cc_start: 0.9364 (mtm) cc_final: 0.9155 (mtt) REVERT: U 147 MET cc_start: 0.9359 (mtm) cc_final: 0.9151 (mtt) REVERT: V 147 MET cc_start: 0.9356 (mtm) cc_final: 0.9143 (mtt) REVERT: W 147 MET cc_start: 0.9361 (mtm) cc_final: 0.9151 (mtt) REVERT: X 147 MET cc_start: 0.9365 (mtm) cc_final: 0.9156 (mtt) REVERT: Y 147 MET cc_start: 0.9364 (mtm) cc_final: 0.9161 (mtt) outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.7783 time to fit residues: 449.1550 Evaluate side-chains 448 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 1 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 347 optimal weight: 3.9990 chunk 264 optimal weight: 0.0170 chunk 312 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN N 82 GLN O 82 GLN P 82 GLN Q 82 GLN S 82 GLN T 82 GLN U 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.083594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.067614 restraints weight = 182791.323| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.27 r_work: 0.2513 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33648 Z= 0.149 Angle : 0.480 6.472 45408 Z= 0.262 Chirality : 0.039 0.134 4800 Planarity : 0.003 0.027 6072 Dihedral : 3.940 14.068 4416 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.72 (0.13), residues: 4056 helix: 4.37 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.39 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 72 TYR 0.021 0.002 TYR U 28 PHE 0.015 0.002 PHE R 35 TRP 0.004 0.001 TRP A 89 HIS 0.002 0.001 HIS L 124 Details of bonding type rmsd covalent geometry : bond 0.00294 (33648) covalent geometry : angle 0.47975 (45408) hydrogen bonds : bond 0.07824 ( 2688) hydrogen bonds : angle 3.47015 ( 8088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14436.53 seconds wall clock time: 245 minutes 15.66 seconds (14715.66 seconds total)