Starting phenix.real_space_refine on Mon Nov 13 22:24:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/11_2023/8tj2_41298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/11_2023/8tj2_41298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/11_2023/8tj2_41298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/11_2023/8tj2_41298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/11_2023/8tj2_41298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/11_2023/8tj2_41298.pdb" } resolution = 3.0 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= 0.007 sd= 0.150 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 S 126 5.16 5 C 17406 2.51 5 N 4824 2.21 5 O 5436 1.98 5 H 26460 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 55": "OD1" <-> "OD2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D ASP 118": "OD1" <-> "OD2" Residue "E PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E ASP 146": "OD1" <-> "OD2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "F TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 55": "OD1" <-> "OD2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "F ASP 118": "OD1" <-> "OD2" Residue "F ASP 146": "OD1" <-> "OD2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G ASP 55": "OD1" <-> "OD2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G ASP 146": "OD1" <-> "OD2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 55": "OD1" <-> "OD2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H GLU 86": "OE1" <-> "OE2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H ASP 146": "OD1" <-> "OD2" Residue "H GLU 175": "OE1" <-> "OE2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 59": "OD1" <-> "OD2" Residue "I ASP 118": "OD1" <-> "OD2" Residue "I ASP 146": "OD1" <-> "OD2" Residue "I ASP 167": "OD1" <-> "OD2" Residue "I ASP 168": "OD1" <-> "OD2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "I ASP 200": "OD1" <-> "OD2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J ASP 106": "OD1" <-> "OD2" Residue "J ASP 167": "OD1" <-> "OD2" Residue "J GLU 175": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K ASP 59": "OD1" <-> "OD2" Residue "K GLU 86": "OE1" <-> "OE2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "K ASP 118": "OD1" <-> "OD2" Residue "K GLU 175": "OE1" <-> "OE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "L PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L ASP 55": "OD1" <-> "OD2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L ASP 168": "OD1" <-> "OD2" Residue "L GLU 175": "OE1" <-> "OE2" Residue "M GLU 53": "OE1" <-> "OE2" Residue "M ASP 55": "OD1" <-> "OD2" Residue "M ASP 59": "OD1" <-> "OD2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M GLU 86": "OE1" <-> "OE2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M ASP 118": "OD1" <-> "OD2" Residue "M ASP 167": "OD1" <-> "OD2" Residue "M GLU 175": "OE1" <-> "OE2" Residue "N PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 53": "OE1" <-> "OE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N ASP 59": "OD1" <-> "OD2" Residue "N GLU 63": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N ASP 118": "OD1" <-> "OD2" Residue "N ASP 146": "OD1" <-> "OD2" Residue "N ASP 168": "OD1" <-> "OD2" Residue "O PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O ASP 92": "OD1" <-> "OD2" Residue "O ASP 168": "OD1" <-> "OD2" Residue "P PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "P ASP 59": "OD1" <-> "OD2" Residue "P GLU 63": "OE1" <-> "OE2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ASP 146": "OD1" <-> "OD2" Residue "P ASP 200": "OD1" <-> "OD2" Residue "Q PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 53": "OE1" <-> "OE2" Residue "Q ASP 55": "OD1" <-> "OD2" Residue "Q ASP 59": "OD1" <-> "OD2" Residue "Q ASP 106": "OD1" <-> "OD2" Residue "Q ASP 118": "OD1" <-> "OD2" Residue "Q ASP 146": "OD1" <-> "OD2" Residue "Q ASP 167": "OD1" <-> "OD2" Residue "R ASP 59": "OD1" <-> "OD2" Residue "R GLU 63": "OE1" <-> "OE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R ASP 118": "OD1" <-> "OD2" Residue "R ASP 168": "OD1" <-> "OD2" Residue "R GLU 175": "OE1" <-> "OE2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S ASP 92": "OD1" <-> "OD2" Residue "S ASP 167": "OD1" <-> "OD2" Residue "S GLU 175": "OE1" <-> "OE2" Residue "S ASP 200": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 54252 Number of models: 1 Model: "" Number of chains: 18 Chain: "C" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "D" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "G" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "H" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "I" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "J" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "K" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "L" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "M" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "N" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "O" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "P" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "Q" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "R" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Chain: "S" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3014 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195} Time building chain proxies: 17.17, per 1000 atoms: 0.32 Number of scatterers: 54252 At special positions: 0 Unit cell: (84.24, 84.24, 272.16, 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) S 126 16.00 O 5436 8.00 N 4824 7.00 C 17406 6.00 H 26460 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 85 " - pdb=" SG CYS D 102 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS E 85 " - pdb=" SG CYS E 102 " distance=2.03 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 85 " - pdb=" SG CYS F 102 " distance=2.03 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 85 " - pdb=" SG CYS G 102 " distance=2.03 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 85 " - pdb=" SG CYS H 102 " distance=2.03 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS I 85 " - pdb=" SG CYS I 102 " distance=2.03 Simple disulfide: pdb=" SG CYS I 183 " - pdb=" SG CYS I 203 " distance=2.03 Simple disulfide: pdb=" SG CYS J 85 " - pdb=" SG CYS J 102 " distance=2.03 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 203 " distance=2.03 Simple disulfide: pdb=" SG CYS K 85 " - pdb=" SG CYS K 102 " distance=2.03 Simple disulfide: pdb=" SG CYS K 183 " - pdb=" SG CYS K 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 85 " - pdb=" SG CYS L 102 " distance=2.03 Simple disulfide: pdb=" SG CYS L 183 " - pdb=" SG CYS L 203 " distance=2.03 Simple disulfide: pdb=" SG CYS M 85 " - pdb=" SG CYS M 102 " distance=2.03 Simple disulfide: pdb=" SG CYS M 183 " - pdb=" SG CYS M 203 " distance=2.03 Simple disulfide: pdb=" SG CYS N 85 " - pdb=" SG CYS N 102 " distance=2.03 Simple disulfide: pdb=" SG CYS N 183 " - pdb=" SG CYS N 203 " distance=2.03 Simple disulfide: pdb=" SG CYS O 85 " - pdb=" SG CYS O 102 " distance=2.03 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 203 " distance=2.03 Simple disulfide: pdb=" SG CYS P 85 " - pdb=" SG CYS P 102 " distance=2.03 Simple disulfide: pdb=" SG CYS P 183 " - pdb=" SG CYS P 203 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 85 " - pdb=" SG CYS Q 102 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 183 " - pdb=" SG CYS Q 203 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 102 " distance=2.03 Simple disulfide: pdb=" SG CYS R 183 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 85 " - pdb=" SG CYS S 102 " distance=2.03 Simple disulfide: pdb=" SG CYS S 183 " - pdb=" SG CYS S 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 31.29 Conformation dependent library (CDL) restraints added in 4.7 seconds 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 39 sheets defined 29.3% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'C' and resid 2 through 18 removed outlier: 3.534A pdb=" N ALA C 18 " --> pdb=" O GLY C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 33 through 55 removed outlier: 3.769A pdb=" N LYS C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 65 removed outlier: 3.685A pdb=" N ILE C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'D' and resid 2 through 18 removed outlier: 3.519A pdb=" N ALA D 18 " --> pdb=" O GLY D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 33 Processing helix chain 'D' and resid 33 through 55 removed outlier: 3.720A pdb=" N LYS D 37 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.589A pdb=" N ILE D 64 " --> pdb=" O PHE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'E' and resid 2 through 18 removed outlier: 3.570A pdb=" N ALA E 18 " --> pdb=" O GLY E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 Processing helix chain 'E' and resid 33 through 55 removed outlier: 3.767A pdb=" N LYS E 37 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.642A pdb=" N ILE E 64 " --> pdb=" O PHE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 115 removed outlier: 3.548A pdb=" N ALA E 115 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 18 removed outlier: 3.535A pdb=" N ALA F 18 " --> pdb=" O GLY F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 33 through 55 removed outlier: 3.766A pdb=" N LYS F 37 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 65 removed outlier: 3.519A pdb=" N ILE F 64 " --> pdb=" O PHE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'G' and resid 2 through 18 removed outlier: 3.567A pdb=" N ALA G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 Processing helix chain 'G' and resid 33 through 55 removed outlier: 3.807A pdb=" N LYS G 37 " --> pdb=" O GLN G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 removed outlier: 3.547A pdb=" N ILE G 64 " --> pdb=" O PHE G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'H' and resid 2 through 18 Processing helix chain 'H' and resid 24 through 33 Processing helix chain 'H' and resid 33 through 55 removed outlier: 3.784A pdb=" N LYS H 37 " --> pdb=" O GLN H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 removed outlier: 3.654A pdb=" N ILE H 64 " --> pdb=" O PHE H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'I' and resid 2 through 18 removed outlier: 3.502A pdb=" N ALA I 18 " --> pdb=" O GLY I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 33 removed outlier: 4.220A pdb=" N PHE I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 55 removed outlier: 3.795A pdb=" N LYS I 37 " --> pdb=" O GLN I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 3.590A pdb=" N ILE I 64 " --> pdb=" O PHE I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 115 Processing helix chain 'J' and resid 2 through 18 removed outlier: 3.511A pdb=" N ALA J 18 " --> pdb=" O GLY J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 33 Processing helix chain 'J' and resid 33 through 55 removed outlier: 3.784A pdb=" N LYS J 37 " --> pdb=" O GLN J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 65 Processing helix chain 'J' and resid 111 through 115 Processing helix chain 'K' and resid 2 through 18 Processing helix chain 'K' and resid 24 through 33 Processing helix chain 'K' and resid 33 through 55 removed outlier: 3.773A pdb=" N LYS K 37 " --> pdb=" O GLN K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 Processing helix chain 'K' and resid 111 through 115 Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.535A pdb=" N ALA A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 33 through 55 removed outlier: 3.788A pdb=" N LYS A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.674A pdb=" N ILE A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.560A pdb=" N ALA A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 18 Processing helix chain 'L' and resid 24 through 33 Processing helix chain 'L' and resid 33 through 55 removed outlier: 3.796A pdb=" N LYS L 37 " --> pdb=" O GLN L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 65 removed outlier: 3.599A pdb=" N ILE L 64 " --> pdb=" O PHE L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 115 Processing helix chain 'M' and resid 2 through 18 removed outlier: 3.533A pdb=" N ALA M 18 " --> pdb=" O GLY M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 33 Processing helix chain 'M' and resid 33 through 55 removed outlier: 3.796A pdb=" N LYS M 37 " --> pdb=" O GLN M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 65 Processing helix chain 'M' and resid 111 through 115 Processing helix chain 'N' and resid 2 through 18 removed outlier: 3.524A pdb=" N ALA N 18 " --> pdb=" O GLY N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 33 Processing helix chain 'N' and resid 33 through 55 removed outlier: 3.715A pdb=" N LYS N 37 " --> pdb=" O GLN N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 65 removed outlier: 3.556A pdb=" N ILE N 64 " --> pdb=" O PHE N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 115 Processing helix chain 'O' and resid 2 through 17 Processing helix chain 'O' and resid 24 through 33 Processing helix chain 'O' and resid 33 through 55 removed outlier: 3.805A pdb=" N LYS O 37 " --> pdb=" O GLN O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 65 removed outlier: 3.528A pdb=" N ILE O 64 " --> pdb=" O PHE O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'P' and resid 2 through 18 removed outlier: 3.616A pdb=" N ALA P 18 " --> pdb=" O GLY P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 33 removed outlier: 4.232A pdb=" N PHE P 27 " --> pdb=" O ASN P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 55 removed outlier: 3.776A pdb=" N LYS P 37 " --> pdb=" O GLN P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 65 removed outlier: 3.721A pdb=" N ILE P 64 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 115 Processing helix chain 'Q' and resid 2 through 18 Processing helix chain 'Q' and resid 24 through 33 Processing helix chain 'Q' and resid 33 through 55 removed outlier: 3.777A pdb=" N LYS Q 37 " --> pdb=" O GLN Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 65 removed outlier: 3.591A pdb=" N ILE Q 64 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 115 Processing helix chain 'R' and resid 2 through 17 Processing helix chain 'R' and resid 24 through 33 Processing helix chain 'R' and resid 33 through 55 removed outlier: 3.761A pdb=" N LYS R 37 " --> pdb=" O GLN R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 65 removed outlier: 3.566A pdb=" N ILE R 64 " --> pdb=" O PHE R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 115 removed outlier: 3.525A pdb=" N ALA R 115 " --> pdb=" O ALA R 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 18 removed outlier: 3.571A pdb=" N ALA S 18 " --> pdb=" O GLY S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 33 Processing helix chain 'S' and resid 33 through 55 removed outlier: 3.784A pdb=" N LYS S 37 " --> pdb=" O GLN S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 65 removed outlier: 3.637A pdb=" N ILE S 64 " --> pdb=" O PHE S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 115 Processing sheet with id=AA1, first strand: chain 'C' and resid 102 through 103 removed outlier: 7.004A pdb=" N VAL C 170 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASN C 196 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 126 through 128 removed outlier: 3.841A pdb=" N GLY C 187 " --> pdb=" O GLY C 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 102 through 103 removed outlier: 6.378A pdb=" N ASP D 168 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 126 through 128 Processing sheet with id=AA5, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA6, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.517A pdb=" N ARG E 198 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 170 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASN E 196 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 128 removed outlier: 3.881A pdb=" N GLY E 187 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 102 through 103 removed outlier: 6.390A pdb=" N ASP F 168 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 126 through 128 removed outlier: 3.881A pdb=" N GLY F 187 " --> pdb=" O GLY F 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 102 through 103 removed outlier: 6.378A pdb=" N ASP G 168 " --> pdb=" O THR G 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 126 through 128 removed outlier: 3.798A pdb=" N GLY G 187 " --> pdb=" O GLY G 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 102 through 103 removed outlier: 6.410A pdb=" N ASP H 168 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 126 through 128 Processing sheet with id=AB5, first strand: chain 'I' and resid 102 through 103 removed outlier: 6.332A pdb=" N ASP I 168 " --> pdb=" O THR I 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 126 through 128 removed outlier: 3.902A pdb=" N GLY I 187 " --> pdb=" O GLY I 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 102 through 103 Processing sheet with id=AB8, first strand: chain 'J' and resid 102 through 103 removed outlier: 6.438A pdb=" N ASP J 168 " --> pdb=" O THR J 197 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 126 through 128 removed outlier: 3.794A pdb=" N GLY J 187 " --> pdb=" O GLY J 178 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 102 through 103 removed outlier: 6.429A pdb=" N ASP K 168 " --> pdb=" O THR K 197 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 126 through 128 removed outlier: 3.909A pdb=" N GLY K 187 " --> pdb=" O GLY K 178 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 102 through 103 removed outlier: 6.386A pdb=" N ASP A 168 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AC5, first strand: chain 'L' and resid 102 through 103 removed outlier: 6.411A pdb=" N ASP L 168 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 126 through 128 removed outlier: 3.806A pdb=" N GLY L 187 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 102 through 103 removed outlier: 6.400A pdb=" N ASP M 168 " --> pdb=" O THR M 197 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 126 through 128 removed outlier: 3.777A pdb=" N GLY M 187 " --> pdb=" O GLY M 178 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 102 through 103 removed outlier: 7.022A pdb=" N VAL N 170 " --> pdb=" O ASN N 196 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASN N 196 " --> pdb=" O VAL N 170 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 126 through 128 removed outlier: 3.868A pdb=" N GLY N 187 " --> pdb=" O GLY N 178 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 102 through 103 removed outlier: 7.054A pdb=" N VAL O 170 " --> pdb=" O ASN O 196 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASN O 196 " --> pdb=" O VAL O 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 126 through 128 removed outlier: 3.965A pdb=" N GLY O 187 " --> pdb=" O GLY O 178 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 102 through 103 removed outlier: 6.402A pdb=" N ASP P 168 " --> pdb=" O THR P 197 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 126 through 128 removed outlier: 3.878A pdb=" N GLY P 187 " --> pdb=" O GLY P 178 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 102 through 103 removed outlier: 6.420A pdb=" N ASP Q 168 " --> pdb=" O THR Q 197 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 126 through 128 removed outlier: 3.830A pdb=" N GLY Q 187 " --> pdb=" O GLY Q 178 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 102 through 103 Processing sheet with id=AD9, first strand: chain 'R' and resid 102 through 103 removed outlier: 6.400A pdb=" N ASP R 168 " --> pdb=" O THR R 197 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 126 through 128 removed outlier: 3.870A pdb=" N GLY R 187 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 102 through 103 removed outlier: 6.357A pdb=" N ASP S 168 " --> pdb=" O THR S 197 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 126 through 128 removed outlier: 3.983A pdb=" N GLY S 187 " --> pdb=" O GLY S 178 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 2988 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: 16.84 Time building geometry restraints manager: 33.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26424 1.03 - 1.23: 460 1.23 - 1.42: 11870 1.42 - 1.62: 15966 1.62 - 1.81: 144 Bond restraints: 54864 Sorted by residual: bond pdb=" CB PRO J 148 " pdb=" CG PRO J 148 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.21e+00 bond pdb=" CB PRO E 148 " pdb=" CG PRO E 148 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.18e+00 bond pdb=" CB ASN D 199 " pdb=" CG ASN D 199 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.94e+00 bond pdb=" CB ASN A 199 " pdb=" CG ASN A 199 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.91e+00 bond pdb=" CB ASN H 199 " pdb=" CG ASN H 199 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.79e+00 ... (remaining 54859 not shown) Histogram of bond angle deviations from ideal: 64.33 - 79.25: 36 79.25 - 94.16: 0 94.16 - 109.07: 27880 109.07 - 123.98: 67421 123.98 - 138.90: 3321 Bond angle restraints: 98658 Sorted by residual: angle pdb=" C SER F 184 " pdb=" N GLU F 185 " pdb=" H GLU F 185 " ideal model delta sigma weight residual 124.11 73.72 50.39 3.00e+00 1.11e-01 2.82e+02 angle pdb=" C SER I 184 " pdb=" N GLU I 185 " pdb=" H GLU I 185 " ideal model delta sigma weight residual 124.11 74.02 50.10 3.00e+00 1.11e-01 2.79e+02 angle pdb=" C SER G 184 " pdb=" N GLU G 185 " pdb=" H GLU G 185 " ideal model delta sigma weight residual 124.11 74.02 50.09 3.00e+00 1.11e-01 2.79e+02 angle pdb=" C SER A 184 " pdb=" N GLU A 185 " pdb=" H GLU A 185 " ideal model delta sigma weight residual 124.11 74.03 50.08 3.00e+00 1.11e-01 2.79e+02 angle pdb=" C SER S 184 " pdb=" N GLU S 185 " pdb=" H GLU S 185 " ideal model delta sigma weight residual 124.11 74.06 50.06 3.00e+00 1.11e-01 2.78e+02 ... (remaining 98653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 20240 17.05 - 34.10: 1380 34.10 - 51.14: 400 51.14 - 68.19: 95 68.19 - 85.24: 7 Dihedral angle restraints: 22122 sinusoidal: 9666 harmonic: 12456 Sorted by residual: dihedral pdb=" CB CYS C 183 " pdb=" SG CYS C 183 " pdb=" SG CYS C 203 " pdb=" CB CYS C 203 " ideal model delta sinusoidal sigma weight residual 93.00 134.48 -41.48 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CB CYS A 183 " pdb=" SG CYS A 183 " pdb=" SG CYS A 203 " pdb=" CB CYS A 203 " ideal model delta sinusoidal sigma weight residual 93.00 134.37 -41.37 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CB CYS S 183 " pdb=" SG CYS S 183 " pdb=" SG CYS S 203 " pdb=" CB CYS S 203 " ideal model delta sinusoidal sigma weight residual 93.00 134.12 -41.12 1 1.00e+01 1.00e-02 2.37e+01 ... (remaining 22119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2042 0.028 - 0.057: 1345 0.057 - 0.085: 510 0.085 - 0.113: 219 0.113 - 0.142: 78 Chirality restraints: 4194 Sorted by residual: chirality pdb=" CA ILE H 116 " pdb=" N ILE H 116 " pdb=" C ILE H 116 " pdb=" CB ILE H 116 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE G 116 " pdb=" N ILE G 116 " pdb=" C ILE G 116 " pdb=" CB ILE G 116 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE C 21 " pdb=" N ILE C 21 " pdb=" C ILE C 21 " pdb=" CB ILE C 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 4191 not shown) Planarity restraints: 8820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS J 147 " 0.123 5.00e-02 4.00e+02 1.79e-01 5.12e+01 pdb=" N PRO J 148 " -0.309 5.00e-02 4.00e+02 pdb=" CA PRO J 148 " 0.095 5.00e-02 4.00e+02 pdb=" CD PRO J 148 " 0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS M 147 " 0.108 5.00e-02 4.00e+02 1.62e-01 4.20e+01 pdb=" N PRO M 148 " -0.280 5.00e-02 4.00e+02 pdb=" CA PRO M 148 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO M 148 " 0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 147 " -0.107 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO E 148 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO E 148 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO E 148 " -0.084 5.00e-02 4.00e+02 ... (remaining 8817 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 1019 2.09 - 2.72: 91414 2.72 - 3.35: 152453 3.35 - 3.97: 203749 3.97 - 4.60: 327931 Nonbonded interactions: 776566 Sorted by model distance: nonbonded pdb=" H GLU F 185 " pdb=" HA GLU F 185 " model vdw 1.468 1.816 nonbonded pdb=" H GLU A 185 " pdb=" HA GLU A 185 " model vdw 1.476 1.816 nonbonded pdb=" H GLU G 185 " pdb=" HA GLU G 185 " model vdw 1.479 1.816 nonbonded pdb=" H GLU N 185 " pdb=" HA GLU N 185 " model vdw 1.481 1.816 nonbonded pdb=" H GLU O 185 " pdb=" HA GLU O 185 " model vdw 1.485 1.816 ... (remaining 776561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.740 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: 0.630 Extract box with map and model: 5.410 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 124.420 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.270 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:9.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.006 0.114 28404 Z= 0.383 Angle : 0.791 16.827 38682 Z= 0.454 Chirality : 0.045 0.142 4194 Planarity : 0.006 0.179 5310 Dihedral : 13.711 85.242 9972 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.67 % Allowed : 15.81 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 3708 helix: 1.10 (0.17), residues: 882 sheet: -0.10 (0.20), residues: 594 loop : -1.87 (0.10), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 415 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 35 residues processed: 457 average time/residue: 1.8417 time to fit residues: 1037.8103 Evaluate side-chains 405 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 370 time to evaluate : 3.071 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 35 residues processed: 1 average time/residue: 0.5367 time to fit residues: 4.7101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 326 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: D 179 GLN H 151 ASN H 179 GLN K 179 GLN M 179 GLN N 179 GLN Q 129 GLN R 179 GLN S 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 28404 Z= 0.387 Angle : 0.699 20.702 38682 Z= 0.386 Chirality : 0.046 0.150 4194 Planarity : 0.005 0.113 5310 Dihedral : 5.045 19.225 4014 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.53 % Allowed : 14.71 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 3708 helix: 1.12 (0.18), residues: 882 sheet: -0.11 (0.18), residues: 774 loop : -2.00 (0.11), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 382 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 60 residues processed: 459 average time/residue: 1.9426 time to fit residues: 1086.9829 Evaluate side-chains 439 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 379 time to evaluate : 3.100 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 50 residues processed: 11 average time/residue: 1.0759 time to fit residues: 20.2128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 327 optimal weight: 4.9990 chunk 353 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN G 179 GLN H 39 ASN H 151 ASN H 179 GLN I 39 ASN I 129 GLN J 179 GLN K 179 GLN L 39 ASN M 179 GLN O 129 GLN Q 39 ASN R 39 ASN R 151 ASN R 179 GLN S 39 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28404 Z= 0.208 Angle : 0.630 21.364 38682 Z= 0.345 Chirality : 0.043 0.143 4194 Planarity : 0.004 0.087 5310 Dihedral : 4.649 19.349 4014 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.88 % Allowed : 14.39 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 3708 helix: 1.45 (0.18), residues: 882 sheet: -0.13 (0.18), residues: 774 loop : -1.89 (0.11), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 423 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 56 residues processed: 496 average time/residue: 1.8766 time to fit residues: 1143.3302 Evaluate side-chains 455 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 399 time to evaluate : 3.068 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 54 residues processed: 4 average time/residue: 0.4816 time to fit residues: 7.2859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 4.9990 chunk 246 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 347 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN F 129 GLN G 179 GLN H 151 ASN H 179 GLN J 179 GLN K 179 GLN M 179 GLN N 179 GLN P 179 GLN R 179 GLN S 179 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 28404 Z= 0.466 Angle : 0.722 20.911 38682 Z= 0.401 Chirality : 0.047 0.154 4194 Planarity : 0.005 0.082 5310 Dihedral : 5.185 21.339 4014 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.81 % Allowed : 15.14 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.12), residues: 3708 helix: 0.98 (0.17), residues: 882 sheet: 0.19 (0.19), residues: 720 loop : -2.19 (0.11), residues: 2106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 386 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 71 residues processed: 476 average time/residue: 2.0366 time to fit residues: 1182.1928 Evaluate side-chains 442 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 371 time to evaluate : 3.066 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 61 residues processed: 10 average time/residue: 0.8933 time to fit residues: 17.0920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN F 129 GLN G 39 ASN G 179 GLN H 151 ASN J 151 ASN J 179 GLN K 151 ASN K 179 GLN M 179 GLN P 129 GLN R 151 ASN R 179 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28404 Z= 0.350 Angle : 0.675 21.253 38682 Z= 0.372 Chirality : 0.045 0.151 4194 Planarity : 0.005 0.080 5310 Dihedral : 5.080 22.403 4014 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.42 % Allowed : 15.71 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 3708 helix: 1.14 (0.18), residues: 882 sheet: 0.13 (0.19), residues: 720 loop : -2.21 (0.11), residues: 2106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 401 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 77 residues processed: 483 average time/residue: 1.9669 time to fit residues: 1155.2320 Evaluate side-chains 469 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 392 time to evaluate : 3.113 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 66 residues processed: 13 average time/residue: 0.8337 time to fit residues: 20.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.7980 chunk 313 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 348 optimal weight: 6.9990 chunk 289 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN C 179 GLN E 39 ASN F 39 ASN G 179 GLN H 129 GLN H 151 ASN J 39 ASN J 151 ASN J 179 GLN K 39 ASN K 151 ASN K 179 GLN A 39 ASN M 39 ASN M 179 GLN N 39 ASN N 179 GLN O 39 ASN P 129 GLN P 179 GLN R 151 ASN R 179 GLN S 179 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28404 Z= 0.179 Angle : 0.618 21.718 38682 Z= 0.338 Chirality : 0.042 0.143 4194 Planarity : 0.004 0.072 5310 Dihedral : 4.628 20.683 4014 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.13 % Allowed : 16.42 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3708 helix: 1.55 (0.18), residues: 882 sheet: -0.30 (0.19), residues: 774 loop : -1.99 (0.11), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 417 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 68 residues processed: 495 average time/residue: 1.9292 time to fit residues: 1174.0064 Evaluate side-chains 477 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 409 time to evaluate : 3.122 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 67 residues processed: 3 average time/residue: 0.5671 time to fit residues: 7.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 198 optimal weight: 0.4980 chunk 254 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 346 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN D 179 GLN H 151 ASN H 179 GLN I 135 ASN J 151 ASN J 179 GLN K 151 ASN K 179 GLN M 179 GLN R 151 ASN R 179 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28404 Z= 0.219 Angle : 0.622 21.530 38682 Z= 0.341 Chirality : 0.043 0.146 4194 Planarity : 0.004 0.069 5310 Dihedral : 4.526 19.976 4014 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.17 % Allowed : 16.49 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 3708 helix: 1.60 (0.18), residues: 882 sheet: -0.30 (0.19), residues: 774 loop : -1.95 (0.11), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 407 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 74 residues processed: 486 average time/residue: 1.9788 time to fit residues: 1179.7099 Evaluate side-chains 470 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 396 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 67 residues processed: 8 average time/residue: 0.9304 time to fit residues: 15.1040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 171 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 272 optimal weight: 0.5980 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 179 GLN H 151 ASN I 135 ASN J 151 ASN J 179 GLN M 179 GLN N 179 GLN R 151 ASN R 179 GLN S 179 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28404 Z= 0.220 Angle : 0.622 21.467 38682 Z= 0.341 Chirality : 0.042 0.146 4194 Planarity : 0.004 0.067 5310 Dihedral : 4.493 20.131 4014 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.99 % Allowed : 16.81 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3708 helix: 1.67 (0.18), residues: 882 sheet: -0.34 (0.19), residues: 774 loop : -1.94 (0.11), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 400 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 72 residues processed: 477 average time/residue: 1.9199 time to fit residues: 1121.1556 Evaluate side-chains 467 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 395 time to evaluate : 3.053 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 68 residues processed: 4 average time/residue: 0.5711 time to fit residues: 7.7780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 3.9990 chunk 332 optimal weight: 0.7980 chunk 303 optimal weight: 4.9990 chunk 323 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN D 179 GLN G 179 GLN H 151 ASN H 179 GLN I 135 ASN J 151 ASN J 179 GLN K 151 ASN M 179 GLN R 151 ASN R 179 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 28404 Z= 0.259 Angle : 0.634 21.352 38682 Z= 0.348 Chirality : 0.043 0.147 4194 Planarity : 0.004 0.066 5310 Dihedral : 4.550 20.194 4014 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.06 % Allowed : 16.49 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 3708 helix: 1.63 (0.18), residues: 882 sheet: -0.36 (0.19), residues: 774 loop : -1.97 (0.11), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 397 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 75 residues processed: 474 average time/residue: 2.0140 time to fit residues: 1168.9373 Evaluate side-chains 453 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 378 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 69 residues processed: 7 average time/residue: 1.0541 time to fit residues: 14.2121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.8980 chunk 341 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 237 optimal weight: 0.8980 chunk 358 optimal weight: 0.9990 chunk 330 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN G 179 GLN H 151 ASN I 135 ASN J 151 ASN J 179 GLN K 151 ASN A 129 GLN M 179 GLN N 151 ASN N 179 GLN P 39 ASN P 179 GLN R 151 ASN R 179 GLN S 151 ASN S 179 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 28404 Z= 0.159 Angle : 0.605 21.692 38682 Z= 0.330 Chirality : 0.042 0.142 4194 Planarity : 0.004 0.066 5310 Dihedral : 4.274 23.722 4014 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.74 % Allowed : 16.92 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 3708 helix: 1.91 (0.18), residues: 882 sheet: -0.35 (0.19), residues: 774 loop : -1.85 (0.11), residues: 2052 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 392 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 71 residues processed: 463 average time/residue: 1.9381 time to fit residues: 1094.8865 Evaluate side-chains 457 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 386 time to evaluate : 3.050 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 68 residues processed: 5 average time/residue: 0.9553 time to fit residues: 10.6041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 chunk 293 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN D 179 GLN H 151 ASN H 179 GLN I 135 ASN J 179 GLN K 179 GLN M 179 GLN R 151 ASN R 179 GLN S 151 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.119441 restraints weight = 84982.248| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.30 r_work: 0.3242 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28404 Z= 0.250 Angle : 0.624 21.340 38682 Z= 0.342 Chirality : 0.043 0.147 4194 Planarity : 0.004 0.065 5310 Dihedral : 4.402 19.828 4014 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.67 % Allowed : 17.20 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 3708 helix: 1.78 (0.18), residues: 882 sheet: -0.38 (0.19), residues: 774 loop : -1.89 (0.11), residues: 2052 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16316.88 seconds wall clock time: 281 minutes 29.80 seconds (16889.80 seconds total)