Starting phenix.real_space_refine on Sun Jun 29 11:53:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cu8_26996/06_2025/8cu8_26996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cu8_26996/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cu8_26996/06_2025/8cu8_26996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cu8_26996/06_2025/8cu8_26996.map" model { file = "/net/cci-nas-00/data/ceres_data/8cu8_26996/06_2025/8cu8_26996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cu8_26996/06_2025/8cu8_26996.cif" } resolution = 1.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 36.13, per 1000 atoms: 1.02 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: 8.13 Conformation dependent library (CDL) restraints added in 7.3 seconds 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: 2.83 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: 10.43 Time building geometry restraints manager: 9.57 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 169 or resid 201)) selection = (chain 'C' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'D' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'E' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'F' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'G' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'H' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'I' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'J' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'K' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'L' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'M' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'N' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'O' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'P' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'Q' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'R' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'S' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'T' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'U' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'V' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'W' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'X' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'Y' and (resid 2 through 105 or resid 107 through 169 or resid 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: 2.290 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: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.260 Set scattering table: 0.350 Process input model: 92.360 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (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 TRP 0.005 0.001 TRP I 89 HIS 0.004 0.001 HIS V 114 PHE 0.023 0.003 PHE H 35 TYR 0.071 0.004 TYR Q 28 ARG 0.002 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.14810 ( 2688) hydrogen bonds : angle 3.72622 ( 8088) covalent geometry : bond 0.00526 (33648) covalent geometry : angle 0.64951 (45408) *********************** 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 : 4.076 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: 2.6940 time to fit residues: 2229.4917 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 : 6.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 82 GLN A 167 HIS C 79 GLN C 167 HIS D 79 GLN D 82 GLN 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 167 HIS K 79 GLN K 82 GLN K 167 HIS L 79 GLN L 82 GLN L 167 HIS M 79 GLN M 82 GLN M 167 HIS N 79 GLN N 82 GLN N 167 HIS O 79 GLN O 82 GLN O 167 HIS P 79 GLN P 82 GLN P 167 HIS Q 79 GLN Q 82 GLN Q 167 HIS R 79 GLN R 167 HIS S 79 GLN S 82 GLN S 167 HIS T 79 GLN T 82 GLN T 167 HIS U 79 GLN U 82 GLN U 167 HIS V 79 GLN V 167 HIS W 79 GLN W 82 GLN W 167 HIS X 79 GLN X 82 GLN X 167 HIS Y 79 GLN Y 82 GLN Y 167 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.082799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.066813 restraints weight = 177475.750| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.25 r_work: 0.2495 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9204 moved from start: 0.1035 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= 0.163 Angle : 0.511 6.637 45408 Z= 0.283 Chirality : 0.039 0.144 4800 Planarity : 0.003 0.031 6072 Dihedral : 4.224 14.868 4416 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.13), residues: 4056 helix: 3.46 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.41 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 89 HIS 0.002 0.001 HIS G 120 PHE 0.017 0.002 PHE F 35 TYR 0.041 0.003 TYR Q 28 ARG 0.001 0.000 ARG J 72 Details of bonding type rmsd hydrogen bonds : bond 0.08725 ( 2688) hydrogen bonds : angle 3.55269 ( 8088) covalent geometry : bond 0.00327 (33648) covalent geometry : angle 0.51082 (45408) *********************** 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 600 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 4.087 Fit side-chains REVERT: A 147 MET cc_start: 0.9413 (mtm) cc_final: 0.9163 (mtt) REVERT: C 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9170 (mtt) REVERT: D 147 MET cc_start: 0.9416 (mtm) cc_final: 0.9165 (mtt) REVERT: E 147 MET cc_start: 0.9420 (mtm) cc_final: 0.9171 (mtt) REVERT: F 147 MET cc_start: 0.9420 (mtm) cc_final: 0.9169 (mtt) REVERT: G 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9164 (mtt) REVERT: H 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9171 (mtt) REVERT: I 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9163 (mtt) REVERT: J 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9177 (mtt) REVERT: K 147 MET cc_start: 0.9416 (mtm) cc_final: 0.9167 (mtt) REVERT: L 147 MET cc_start: 0.9416 (mtm) cc_final: 0.9174 (mtt) REVERT: M 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9166 (mtt) REVERT: N 147 MET cc_start: 0.9413 (mtm) cc_final: 0.9169 (mtt) REVERT: O 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9164 (mtt) REVERT: P 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9176 (mtt) REVERT: Q 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9167 (mtt) REVERT: R 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9172 (mtt) REVERT: S 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9169 (mtt) REVERT: T 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9168 (mtt) REVERT: U 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9159 (mtt) REVERT: V 147 MET cc_start: 0.9416 (mtm) cc_final: 0.9166 (mtt) REVERT: W 147 MET cc_start: 0.9411 (mtm) cc_final: 0.9163 (mtt) REVERT: X 147 MET cc_start: 0.9416 (mtm) cc_final: 0.9167 (mtt) REVERT: Y 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9172 (mtt) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 1.8524 time to fit residues: 1289.0831 Evaluate side-chains 678 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 372 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 S 82 GLN S 142 ASN 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 = 0.3016 r_free = 0.3016 target = 0.084714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.068742 restraints weight = 182416.042| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.29 r_work: 0.2537 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33648 Z= 0.141 Angle : 0.484 6.681 45408 Z= 0.262 Chirality : 0.038 0.134 4800 Planarity : 0.003 0.029 6072 Dihedral : 4.054 14.596 4416 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.24 (0.13), residues: 4056 helix: 4.10 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.11 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 89 HIS 0.002 0.001 HIS L 124 PHE 0.015 0.002 PHE H 35 TYR 0.029 0.002 TYR Q 28 ARG 0.001 0.000 ARG U 72 Details of bonding type rmsd hydrogen bonds : bond 0.07564 ( 2688) hydrogen bonds : angle 3.43379 ( 8088) covalent geometry : bond 0.00268 (33648) covalent geometry : angle 0.48443 (45408) *********************** 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 685 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 4.140 Fit side-chains REVERT: A 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9163 (mtt) REVERT: C 147 MET cc_start: 0.9399 (mtm) cc_final: 0.9162 (mtt) REVERT: D 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9166 (mtt) REVERT: E 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9172 (mtt) REVERT: F 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9167 (mtt) REVERT: G 147 MET cc_start: 0.9399 (mtm) cc_final: 0.9169 (mtt) REVERT: H 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9162 (mtt) REVERT: I 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9161 (mtt) REVERT: J 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9175 (mtt) REVERT: K 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9165 (mtt) REVERT: L 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9173 (mtt) REVERT: M 147 MET cc_start: 0.9400 (mtm) cc_final: 0.9166 (mtt) REVERT: N 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9164 (mtt) REVERT: O 147 MET cc_start: 0.9400 (mtm) cc_final: 0.9165 (mtt) REVERT: P 147 MET cc_start: 0.9400 (mtm) cc_final: 0.9171 (mtt) REVERT: Q 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9172 (mtt) REVERT: R 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9165 (mtt) REVERT: S 147 MET cc_start: 0.9397 (mtm) cc_final: 0.9167 (mtt) REVERT: T 147 MET cc_start: 0.9399 (mtm) cc_final: 0.9162 (mtt) REVERT: U 147 MET cc_start: 0.9391 (mtm) cc_final: 0.9155 (mtt) REVERT: V 147 MET cc_start: 0.9400 (mtm) cc_final: 0.9164 (mtt) REVERT: W 147 MET cc_start: 0.9397 (mtm) cc_final: 0.9163 (mtt) REVERT: X 147 MET cc_start: 0.9399 (mtm) cc_final: 0.9163 (mtt) REVERT: Y 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9172 (mtt) outliers start: 0 outliers final: 0 residues processed: 685 average time/residue: 1.8761 time to fit residues: 1494.5383 Evaluate side-chains 539 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 4.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 301 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 379 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.2993 r_free = 0.2993 target = 0.082903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.067103 restraints weight = 187461.309| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.27 r_work: 0.2508 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- 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 = 0.41 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: 0.9194 moved from start: 0.1212 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= 0.153 Angle : 0.509 6.345 45408 Z= 0.272 Chirality : 0.039 0.138 4800 Planarity : 0.003 0.028 6072 Dihedral : 4.021 14.290 4416 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.14 % Allowed : 9.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.37 (0.13), residues: 4056 helix: 4.19 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.07 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 89 HIS 0.002 0.001 HIS A 114 PHE 0.016 0.002 PHE P 35 TYR 0.028 0.002 TYR Q 28 ARG 0.001 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.08079 ( 2688) hydrogen bonds : angle 3.51787 ( 8088) covalent geometry : bond 0.00303 (33648) covalent geometry : angle 0.50928 (45408) *********************** 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 505 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 500 time to evaluate : 4.795 Fit side-chains REVERT: A 147 MET cc_start: 0.9394 (mtm) cc_final: 0.9153 (mtt) REVERT: C 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9164 (mtt) REVERT: D 147 MET cc_start: 0.9400 (mtm) cc_final: 0.9161 (mtt) REVERT: E 147 MET cc_start: 0.9412 (mtm) cc_final: 0.9170 (mtt) REVERT: F 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9165 (mtt) REVERT: G 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9168 (mtt) REVERT: H 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9163 (mtt) REVERT: I 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9159 (mtt) REVERT: J 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9169 (mtt) REVERT: K 147 MET cc_start: 0.9395 (mtm) cc_final: 0.9159 (mtt) REVERT: L 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9166 (mtt) REVERT: M 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9160 (mtt) REVERT: N 147 MET cc_start: 0.9399 (mtm) cc_final: 0.9161 (mtt) REVERT: O 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9160 (mtt) REVERT: P 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9170 (mtt) REVERT: Q 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9171 (mtt) REVERT: R 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9163 (mtt) REVERT: S 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9160 (mtt) REVERT: T 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9162 (mtt) REVERT: U 147 MET cc_start: 0.9397 (mtm) cc_final: 0.9155 (mtt) REVERT: V 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9156 (mtt) REVERT: W 147 MET cc_start: 0.9400 (mtm) cc_final: 0.9159 (mtt) REVERT: X 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9162 (mtt) REVERT: Y 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9168 (mtt) outliers start: 5 outliers final: 0 residues processed: 500 average time/residue: 1.9800 time to fit residues: 1159.5679 Evaluate side-chains 476 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 5.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 147 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 chunk 350 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 367 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN D 142 ASN E 82 GLN F 82 GLN F 142 ASN G 82 GLN H 82 GLN H 142 ASN I 142 ASN J 82 GLN J 142 ASN K 142 ASN M 142 ASN N 82 GLN N 142 ASN O 82 GLN O 142 ASN P 82 GLN P 142 ASN Q 142 ASN R 142 ASN S 82 GLN T 82 GLN U 82 GLN U 142 ASN V 142 ASN W 82 GLN W 142 ASN X 82 GLN Y 82 GLN Y 142 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.087440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.071497 restraints weight = 171932.322| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.19 r_work: 0.2578 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.1530 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= 0.125 Angle : 0.473 6.554 45408 Z= 0.250 Chirality : 0.037 0.127 4800 Planarity : 0.002 0.028 6072 Dihedral : 3.903 14.236 4416 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.09 % Allowed : 10.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.72 (0.13), residues: 4056 helix: 4.41 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.15 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 89 HIS 0.001 0.000 HIS Y 167 PHE 0.014 0.002 PHE E 35 TYR 0.017 0.002 TYR J 28 ARG 0.001 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.06431 ( 2688) hydrogen bonds : angle 3.28696 ( 8088) covalent geometry : bond 0.00230 (33648) covalent geometry : angle 0.47258 (45408) *********************** 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 518 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 515 time to evaluate : 4.392 Fit side-chains REVERT: A 147 MET cc_start: 0.9376 (mtm) cc_final: 0.9162 (mtt) REVERT: C 147 MET cc_start: 0.9378 (mtm) cc_final: 0.9159 (mtt) REVERT: D 131 GLU cc_start: 0.8392 (tp30) cc_final: 0.8042 (tp30) REVERT: D 147 MET cc_start: 0.9369 (mtm) cc_final: 0.9149 (mtt) REVERT: E 147 MET cc_start: 0.9381 (mtm) cc_final: 0.9166 (mtt) REVERT: F 147 MET cc_start: 0.9367 (mtm) cc_final: 0.9152 (mtt) REVERT: G 147 MET cc_start: 0.9364 (mtm) cc_final: 0.9148 (mtt) REVERT: H 147 MET cc_start: 0.9362 (mtm) cc_final: 0.9140 (mtt) REVERT: I 131 GLU cc_start: 0.8442 (tp30) cc_final: 0.8072 (tp30) REVERT: I 147 MET cc_start: 0.9371 (mtm) cc_final: 0.9150 (mtt) REVERT: J 147 MET cc_start: 0.9367 (mtm) cc_final: 0.9151 (mtt) REVERT: K 131 GLU cc_start: 0.8434 (tp30) cc_final: 0.8068 (tp30) REVERT: K 147 MET cc_start: 0.9376 (mtm) cc_final: 0.9158 (mtt) REVERT: L 147 MET cc_start: 0.9368 (mtm) cc_final: 0.9154 (mtt) REVERT: M 147 MET cc_start: 0.9365 (mtm) cc_final: 0.9145 (mtt) REVERT: N 147 MET cc_start: 0.9358 (mtm) cc_final: 0.9141 (mtt) REVERT: O 131 GLU cc_start: 0.8431 (tp30) cc_final: 0.8062 (tp30) REVERT: O 147 MET cc_start: 0.9366 (mtm) cc_final: 0.9151 (mtt) REVERT: P 147 MET cc_start: 0.9365 (mtm) cc_final: 0.9151 (mtt) REVERT: Q 131 GLU cc_start: 0.8451 (tp30) cc_final: 0.8085 (tp30) REVERT: Q 147 MET cc_start: 0.9372 (mtm) cc_final: 0.9151 (mtt) REVERT: R 147 MET cc_start: 0.9360 (mtm) cc_final: 0.9144 (mtt) REVERT: S 147 MET cc_start: 0.9364 (mtm) cc_final: 0.9147 (mtt) REVERT: T 147 MET cc_start: 0.9368 (mtm) cc_final: 0.9152 (mtt) REVERT: U 147 MET cc_start: 0.9375 (mtm) cc_final: 0.9159 (mtt) REVERT: V 147 MET cc_start: 0.9368 (mtm) cc_final: 0.9150 (mtt) REVERT: W 147 MET cc_start: 0.9374 (mtm) cc_final: 0.9160 (mtt) REVERT: X 147 MET cc_start: 0.9366 (mtm) cc_final: 0.9145 (mtt) REVERT: Y 147 MET cc_start: 0.9369 (mtm) cc_final: 0.9156 (mtt) outliers start: 3 outliers final: 0 residues processed: 515 average time/residue: 2.0791 time to fit residues: 1258.5231 Evaluate side-chains 489 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 6.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 183 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 304 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3028 r_free = 0.3028 target = 0.084937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.068690 restraints weight = 201224.207| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.32 r_work: 0.2536 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.1374 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= 0.141 Angle : 0.484 6.361 45408 Z= 0.260 Chirality : 0.038 0.132 4800 Planarity : 0.002 0.027 6072 Dihedral : 3.922 14.004 4416 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.69 (0.13), residues: 4056 helix: 4.37 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : 0.26 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 89 HIS 0.002 0.001 HIS A 114 PHE 0.015 0.002 PHE Q 35 TYR 0.020 0.002 TYR F 28 ARG 0.001 0.000 ARG G 72 Details of bonding type rmsd hydrogen bonds : bond 0.07429 ( 2688) hydrogen bonds : angle 3.42643 ( 8088) covalent geometry : bond 0.00270 (33648) covalent geometry : angle 0.48434 (45408) *********************** 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 509 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 3.994 Fit side-chains REVERT: A 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9164 (mtt) REVERT: C 131 GLU cc_start: 0.8476 (tp30) cc_final: 0.8126 (tp30) REVERT: C 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9171 (mtt) REVERT: D 131 GLU cc_start: 0.8379 (tp30) cc_final: 0.8091 (tp30) REVERT: D 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9167 (mtt) REVERT: E 131 GLU cc_start: 0.8474 (tp30) cc_final: 0.8105 (tp30) REVERT: E 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9181 (mtt) REVERT: F 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9170 (mtt) REVERT: G 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9173 (mtt) REVERT: H 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9172 (mtt) REVERT: I 131 GLU cc_start: 0.8477 (tp30) cc_final: 0.8180 (tp30) REVERT: I 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9169 (mtt) REVERT: J 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9177 (mtt) REVERT: K 131 GLU cc_start: 0.8488 (tp30) cc_final: 0.8189 (tp30) REVERT: K 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9166 (mtt) REVERT: L 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9170 (mtt) REVERT: M 131 GLU cc_start: 0.8446 (tp30) cc_final: 0.8101 (tp30) REVERT: M 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9175 (mtt) REVERT: N 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9169 (mtt) REVERT: O 131 GLU cc_start: 0.8454 (tp30) cc_final: 0.8157 (tp30) REVERT: O 147 MET cc_start: 0.9402 (mtm) cc_final: 0.9167 (mtt) REVERT: P 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9176 (mtt) REVERT: Q 131 GLU cc_start: 0.8479 (tp30) cc_final: 0.8178 (tp30) REVERT: Q 147 MET cc_start: 0.9412 (mtm) cc_final: 0.9177 (mtt) REVERT: R 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9175 (mtt) REVERT: S 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9172 (mtt) REVERT: T 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9172 (mtt) REVERT: U 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9170 (mtt) REVERT: V 147 MET cc_start: 0.9398 (mtm) cc_final: 0.9163 (mtt) REVERT: W 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9175 (mtt) REVERT: X 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9169 (mtt) REVERT: Y 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9179 (mtt) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 1.7652 time to fit residues: 1052.9945 Evaluate side-chains 503 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 254 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 355 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.2960 r_free = 0.2960 target = 0.081067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.065127 restraints weight = 182106.689| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.27 r_work: 0.2458 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9222 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 33648 Z= 0.189 Angle : 0.533 6.346 45408 Z= 0.291 Chirality : 0.041 0.147 4800 Planarity : 0.003 0.028 6072 Dihedral : 4.061 14.366 4416 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.37 (0.13), residues: 4056 helix: 4.15 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.18 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 89 HIS 0.003 0.001 HIS U 114 PHE 0.018 0.002 PHE L 35 TYR 0.028 0.003 TYR F 28 ARG 0.001 0.000 ARG R 72 Details of bonding type rmsd hydrogen bonds : bond 0.09186 ( 2688) hydrogen bonds : angle 3.67049 ( 8088) covalent geometry : bond 0.00410 (33648) covalent geometry : angle 0.53269 (45408) *********************** 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 474 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 3.882 Fit side-chains REVERT: A 147 MET cc_start: 0.9415 (mtm) cc_final: 0.9171 (mtt) REVERT: C 131 GLU cc_start: 0.8513 (tp30) cc_final: 0.8094 (tp30) REVERT: C 147 MET cc_start: 0.9426 (mtm) cc_final: 0.9179 (mtt) REVERT: D 131 GLU cc_start: 0.8386 (tp30) cc_final: 0.8086 (tp30) REVERT: D 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9169 (mtt) REVERT: E 131 GLU cc_start: 0.8497 (tp30) cc_final: 0.8073 (tp30) REVERT: E 147 MET cc_start: 0.9429 (mtm) cc_final: 0.9184 (mtt) REVERT: F 147 MET cc_start: 0.9422 (mtm) cc_final: 0.9175 (mtt) REVERT: G 147 MET cc_start: 0.9424 (mtm) cc_final: 0.9165 (mtt) REVERT: H 147 MET cc_start: 0.9420 (mtm) cc_final: 0.9174 (mtt) REVERT: I 131 GLU cc_start: 0.8458 (tp30) cc_final: 0.8167 (tp30) REVERT: I 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9173 (mtt) REVERT: J 147 MET cc_start: 0.9426 (mtm) cc_final: 0.9167 (mtt) REVERT: K 131 GLU cc_start: 0.8462 (tp30) cc_final: 0.8171 (tp30) REVERT: K 147 MET cc_start: 0.9420 (mtm) cc_final: 0.9174 (mtt) REVERT: L 147 MET cc_start: 0.9424 (mtm) cc_final: 0.9165 (mtt) REVERT: M 131 GLU cc_start: 0.8488 (tp30) cc_final: 0.8076 (tp30) REVERT: M 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9174 (mtt) REVERT: N 147 MET cc_start: 0.9420 (mtm) cc_final: 0.9160 (mtt) REVERT: O 131 GLU cc_start: 0.8440 (tp30) cc_final: 0.8151 (tp30) REVERT: O 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9175 (mtt) REVERT: P 147 MET cc_start: 0.9427 (mtm) cc_final: 0.9171 (mtt) REVERT: Q 131 GLU cc_start: 0.8468 (tp30) cc_final: 0.8175 (tp30) REVERT: Q 147 MET cc_start: 0.9431 (mtm) cc_final: 0.9184 (mtt) REVERT: R 147 MET cc_start: 0.9420 (mtm) cc_final: 0.9163 (mtt) REVERT: S 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9161 (mtt) REVERT: T 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9174 (mtt) REVERT: U 147 MET cc_start: 0.9418 (mtm) cc_final: 0.9158 (mtt) REVERT: V 147 MET cc_start: 0.9421 (mtm) cc_final: 0.9160 (mtt) REVERT: W 147 MET cc_start: 0.9422 (mtm) cc_final: 0.9163 (mtt) REVERT: X 147 MET cc_start: 0.9422 (mtm) cc_final: 0.9175 (mtt) REVERT: Y 147 MET cc_start: 0.9423 (mtm) cc_final: 0.9167 (mtt) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 1.7677 time to fit residues: 975.6366 Evaluate side-chains 473 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 323 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 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 V 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.082470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.066586 restraints weight = 188076.264| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.27 r_work: 0.2494 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9201 moved from start: 0.1255 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= 0.159 Angle : 0.507 6.324 45408 Z= 0.274 Chirality : 0.040 0.143 4800 Planarity : 0.003 0.027 6072 Dihedral : 4.015 14.092 4416 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.51 (0.13), residues: 4056 helix: 4.24 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : 0.23 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 89 HIS 0.002 0.001 HIS L 114 PHE 0.018 0.002 PHE W 35 TYR 0.023 0.002 TYR V 28 ARG 0.001 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.08226 ( 2688) hydrogen bonds : angle 3.56230 ( 8088) covalent geometry : bond 0.00321 (33648) covalent geometry : angle 0.50655 (45408) *********************** 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 477 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 3.999 Fit side-chains REVERT: A 147 MET cc_start: 0.9401 (mtm) cc_final: 0.9159 (mtt) REVERT: C 131 GLU cc_start: 0.8509 (tp30) cc_final: 0.8095 (tp30) REVERT: C 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9163 (mtt) REVERT: D 131 GLU cc_start: 0.8428 (tp30) cc_final: 0.8107 (tp30) REVERT: D 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9160 (mtt) REVERT: E 131 GLU cc_start: 0.8480 (tp30) cc_final: 0.8065 (tp30) REVERT: E 147 MET cc_start: 0.9417 (mtm) cc_final: 0.9174 (mtt) REVERT: F 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9164 (mtt) REVERT: G 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9166 (mtt) REVERT: H 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9163 (mtt) REVERT: I 131 GLU cc_start: 0.8460 (tp30) cc_final: 0.8165 (tp30) REVERT: I 147 MET cc_start: 0.9410 (mtm) cc_final: 0.9163 (mtt) REVERT: J 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9166 (mtt) REVERT: K 131 GLU cc_start: 0.8461 (tp30) cc_final: 0.8167 (tp30) REVERT: K 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9162 (mtt) REVERT: L 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9165 (mtt) REVERT: M 131 GLU cc_start: 0.8483 (tp30) cc_final: 0.8075 (tp30) REVERT: M 147 MET cc_start: 0.9411 (mtm) cc_final: 0.9164 (mtt) REVERT: N 147 MET cc_start: 0.9403 (mtm) cc_final: 0.9160 (mtt) REVERT: O 131 GLU cc_start: 0.8444 (tp30) cc_final: 0.8152 (tp30) REVERT: O 147 MET cc_start: 0.9405 (mtm) cc_final: 0.9160 (mtt) REVERT: P 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9175 (mtt) REVERT: Q 131 GLU cc_start: 0.8471 (tp30) cc_final: 0.8175 (tp30) REVERT: Q 147 MET cc_start: 0.9414 (mtm) cc_final: 0.9168 (mtt) REVERT: R 147 MET cc_start: 0.9404 (mtm) cc_final: 0.9162 (mtt) REVERT: S 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9162 (mtt) REVERT: T 147 MET cc_start: 0.9406 (mtm) cc_final: 0.9158 (mtt) REVERT: U 147 MET cc_start: 0.9407 (mtm) cc_final: 0.9166 (mtt) REVERT: V 147 MET cc_start: 0.9408 (mtm) cc_final: 0.9166 (mtt) REVERT: W 147 MET cc_start: 0.9409 (mtm) cc_final: 0.9169 (mtt) REVERT: X 147 MET cc_start: 0.9411 (mtm) cc_final: 0.9164 (mtt) REVERT: Y 147 MET cc_start: 0.9413 (mtm) cc_final: 0.9174 (mtt) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 1.9196 time to fit residues: 1065.2214 Evaluate side-chains 471 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 81 optimal weight: 0.9990 chunk 271 optimal weight: 0.0770 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 353 optimal weight: 0.9980 chunk 241 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 333 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 142 ASN C 142 ASN D 82 GLN E 82 GLN E 142 ASN F 82 GLN G 82 GLN G 142 ASN H 82 GLN J 82 GLN L 82 GLN L 142 ASN M 82 GLN N 82 GLN O 82 GLN P 82 GLN 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.090262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.074459 restraints weight = 174921.085| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.13 r_work: 0.2645 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 33648 Z= 0.113 Angle : 0.455 6.588 45408 Z= 0.239 Chirality : 0.036 0.120 4800 Planarity : 0.002 0.027 6072 Dihedral : 3.843 14.292 4416 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.97 (0.13), residues: 4056 helix: 4.55 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.42 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 89 HIS 0.001 0.000 HIS A 120 PHE 0.011 0.001 PHE I 35 TYR 0.011 0.001 TYR A 28 ARG 0.001 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05482 ( 2688) hydrogen bonds : angle 3.14763 ( 8088) covalent geometry : bond 0.00206 (33648) covalent geometry : angle 0.45461 (45408) *********************** 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 527 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 4.487 Fit side-chains REVERT: A 147 MET cc_start: 0.9343 (mtm) cc_final: 0.9133 (mtt) REVERT: C 131 GLU cc_start: 0.8408 (tp30) cc_final: 0.7976 (tp30) REVERT: C 147 MET cc_start: 0.9346 (mtm) cc_final: 0.9132 (mtt) REVERT: D 131 GLU cc_start: 0.8319 (tp30) cc_final: 0.7960 (tp30) REVERT: D 147 MET cc_start: 0.9344 (mtm) cc_final: 0.9130 (mtt) REVERT: E 131 GLU cc_start: 0.8408 (tp30) cc_final: 0.7975 (tp30) REVERT: E 147 MET cc_start: 0.9354 (mtm) cc_final: 0.9143 (mtt) REVERT: F 147 MET cc_start: 0.9347 (mtm) cc_final: 0.9134 (mtt) REVERT: G 147 MET cc_start: 0.9344 (mtm) cc_final: 0.9133 (mtt) REVERT: H 147 MET cc_start: 0.9342 (mtm) cc_final: 0.9128 (mtt) REVERT: I 131 GLU cc_start: 0.8353 (tp30) cc_final: 0.7960 (tp30) REVERT: I 147 MET cc_start: 0.9351 (mtm) cc_final: 0.9138 (mtt) REVERT: J 147 MET cc_start: 0.9347 (mtm) cc_final: 0.9137 (mtt) REVERT: K 131 GLU cc_start: 0.8354 (tp30) cc_final: 0.7959 (tp30) REVERT: K 147 MET cc_start: 0.9345 (mtm) cc_final: 0.9132 (mtt) REVERT: L 147 MET cc_start: 0.9348 (mtm) cc_final: 0.9137 (mtt) REVERT: M 131 GLU cc_start: 0.8382 (tp30) cc_final: 0.7955 (tp30) REVERT: M 147 MET cc_start: 0.9346 (mtm) cc_final: 0.9133 (mtt) REVERT: N 147 MET cc_start: 0.9337 (mtm) cc_final: 0.9125 (mtt) REVERT: O 131 GLU cc_start: 0.8365 (tp30) cc_final: 0.7975 (tp30) REVERT: O 147 MET cc_start: 0.9345 (mtm) cc_final: 0.9133 (mtt) REVERT: P 147 MET cc_start: 0.9345 (mtm) cc_final: 0.9137 (mtt) REVERT: Q 131 GLU cc_start: 0.8371 (tp30) cc_final: 0.7979 (tp30) REVERT: Q 147 MET cc_start: 0.9351 (mtm) cc_final: 0.9138 (mtt) REVERT: R 147 MET cc_start: 0.9341 (mtm) cc_final: 0.9131 (mtt) REVERT: S 147 MET cc_start: 0.9346 (mtm) cc_final: 0.9128 (mtt) REVERT: T 147 MET cc_start: 0.9347 (mtm) cc_final: 0.9134 (mtt) REVERT: U 147 MET cc_start: 0.9346 (mtm) cc_final: 0.9134 (mtt) REVERT: V 147 MET cc_start: 0.9340 (mtm) cc_final: 0.9128 (mtt) REVERT: W 147 MET cc_start: 0.9350 (mtm) cc_final: 0.9141 (mtt) REVERT: X 147 MET cc_start: 0.9347 (mtm) cc_final: 0.9132 (mtt) REVERT: Y 147 MET cc_start: 0.9352 (mtm) cc_final: 0.9147 (mtt) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 1.7336 time to fit residues: 1076.3366 Evaluate side-chains 451 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 346 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 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 = 0.2941 r_free = 0.2941 target = 0.079761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.063800 restraints weight = 186497.414| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.30 r_work: 0.2433 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9239 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 33648 Z= 0.231 Angle : 0.569 6.483 45408 Z= 0.313 Chirality : 0.044 0.150 4800 Planarity : 0.003 0.028 6072 Dihedral : 4.121 14.480 4416 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.24 (0.13), residues: 4056 helix: 4.05 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.20 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 89 HIS 0.004 0.001 HIS A 124 PHE 0.018 0.003 PHE F 35 TYR 0.032 0.003 TYR V 28 ARG 0.001 0.000 ARG K 72 Details of bonding type rmsd hydrogen bonds : bond 0.09990 ( 2688) hydrogen bonds : angle 3.75745 ( 8088) covalent geometry : bond 0.00529 (33648) covalent geometry : angle 0.56925 (45408) ********************** 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 465 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 4.148 Fit side-chains REVERT: A 147 MET cc_start: 0.9424 (mtm) cc_final: 0.9173 (mtt) REVERT: C 131 GLU cc_start: 0.8524 (tp30) cc_final: 0.8104 (tp30) REVERT: C 147 MET cc_start: 0.9437 (mtm) cc_final: 0.9183 (mtt) REVERT: D 131 GLU cc_start: 0.8445 (tp30) cc_final: 0.8085 (tp30) REVERT: D 147 MET cc_start: 0.9432 (mtm) cc_final: 0.9178 (mtt) REVERT: E 131 GLU cc_start: 0.8525 (tp30) cc_final: 0.8102 (tp30) REVERT: E 147 MET cc_start: 0.9441 (mtm) cc_final: 0.9187 (mtt) REVERT: F 147 MET cc_start: 0.9435 (mtm) cc_final: 0.9181 (mtt) REVERT: G 147 MET cc_start: 0.9433 (mtm) cc_final: 0.9182 (mtt) REVERT: H 147 MET cc_start: 0.9432 (mtm) cc_final: 0.9180 (mtt) REVERT: I 131 GLU cc_start: 0.8422 (tp30) cc_final: 0.8150 (tp30) REVERT: I 147 MET cc_start: 0.9440 (mtm) cc_final: 0.9186 (mtt) REVERT: J 147 MET cc_start: 0.9442 (mtm) cc_final: 0.9190 (mtt) REVERT: K 131 GLU cc_start: 0.8425 (tp30) cc_final: 0.8153 (tp30) REVERT: K 147 MET cc_start: 0.9439 (mtm) cc_final: 0.9186 (mtt) REVERT: L 147 MET cc_start: 0.9440 (mtm) cc_final: 0.9190 (mtt) REVERT: M 131 GLU cc_start: 0.8506 (tp30) cc_final: 0.8088 (tp30) REVERT: M 147 MET cc_start: 0.9437 (mtm) cc_final: 0.9184 (mtt) REVERT: N 147 MET cc_start: 0.9438 (mtm) cc_final: 0.9186 (mtt) REVERT: O 131 GLU cc_start: 0.8396 (tp30) cc_final: 0.8125 (tp30) REVERT: O 147 MET cc_start: 0.9437 (mtm) cc_final: 0.9185 (mtt) REVERT: P 147 MET cc_start: 0.9431 (mtm) cc_final: 0.9179 (mtt) REVERT: Q 131 GLU cc_start: 0.8427 (tp30) cc_final: 0.8154 (tp30) REVERT: Q 147 MET cc_start: 0.9451 (mtm) cc_final: 0.9198 (mtt) REVERT: R 147 MET cc_start: 0.9434 (mtm) cc_final: 0.9184 (mtt) REVERT: S 147 MET cc_start: 0.9435 (mtm) cc_final: 0.9184 (mtt) REVERT: T 147 MET cc_start: 0.9436 (mtm) cc_final: 0.9184 (mtt) REVERT: U 147 MET cc_start: 0.9430 (mtm) cc_final: 0.9178 (mtt) REVERT: V 147 MET cc_start: 0.9431 (mtm) cc_final: 0.9176 (mtt) REVERT: W 147 MET cc_start: 0.9434 (mtm) cc_final: 0.9180 (mtt) REVERT: X 147 MET cc_start: 0.9444 (mtm) cc_final: 0.9190 (mtt) REVERT: Y 147 MET cc_start: 0.9432 (mtm) cc_final: 0.9180 (mtt) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 1.7842 time to fit residues: 975.6875 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 : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 352 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 289 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 357 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.087987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.072073 restraints weight = 194851.633| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.29 r_work: 0.2593 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.1638 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= 0.121 Angle : 0.475 6.919 45408 Z= 0.251 Chirality : 0.038 0.129 4800 Planarity : 0.002 0.027 6072 Dihedral : 3.897 14.656 4416 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.88 (0.13), residues: 4056 helix: 4.48 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.50 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 89 HIS 0.001 0.000 HIS G 120 PHE 0.013 0.001 PHE H 35 TYR 0.011 0.001 TYR O 28 ARG 0.001 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.05926 ( 2688) hydrogen bonds : angle 3.26863 ( 8088) covalent geometry : bond 0.00223 (33648) covalent geometry : angle 0.47480 (45408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35434.74 seconds wall clock time: 613 minutes 42.19 seconds (36822.19 seconds total)