Starting phenix.real_space_refine on Wed Mar 4 11:34:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wtd_66219/03_2026/9wtd_66219.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wtd_66219/03_2026/9wtd_66219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wtd_66219/03_2026/9wtd_66219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wtd_66219/03_2026/9wtd_66219.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wtd_66219/03_2026/9wtd_66219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wtd_66219/03_2026/9wtd_66219.map" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8256 2.51 5 N 2208 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13020 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "B" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "D" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "E" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "F" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "G" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "H" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "I" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "J" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "K" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "L" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Chain: "C" Number of atoms: 1085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 138, 1076 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} bond proxies already assigned to first conformer: 1099 Time building chain proxies: 4.76, per 1000 atoms: 0.37 Number of scatterers: 13020 At special positions: 0 Unit cell: (94.132, 88.54, 116.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2472 8.00 N 2208 7.00 C 8256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 163 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 163 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 51 " distance=2.03 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 171 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 163 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 51 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 171 " distance=2.03 Simple disulfide: pdb=" SG CYS G 146 " - pdb=" SG CYS G 163 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 51 " distance=2.03 Simple disulfide: pdb=" SG CYS H 68 " - pdb=" SG CYS H 171 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 163 " distance=2.03 Simple disulfide: pdb=" SG CYS I 40 " - pdb=" SG CYS I 51 " distance=2.03 Simple disulfide: pdb=" SG CYS I 68 " - pdb=" SG CYS I 171 " distance=2.03 Simple disulfide: pdb=" SG CYS I 146 " - pdb=" SG CYS I 163 " distance=2.03 Simple disulfide: pdb=" SG CYS J 40 " - pdb=" SG CYS J 51 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 171 " distance=2.03 Simple disulfide: pdb=" SG CYS J 146 " - pdb=" SG CYS J 163 " distance=2.03 Simple disulfide: pdb=" SG CYS K 40 " - pdb=" SG CYS K 51 " distance=2.03 Simple disulfide: pdb=" SG CYS K 68 " - pdb=" SG CYS K 171 " distance=2.03 Simple disulfide: pdb=" SG CYS K 146 " - pdb=" SG CYS K 163 " distance=2.03 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 51 " distance=2.03 Simple disulfide: pdb=" SG CYS L 68 " - pdb=" SG CYS L 171 " distance=2.03 Simple disulfide: pdb=" SG CYS L 146 " - pdb=" SG CYS L 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 163 " distance=2.03 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: 1.17 Conformation dependent library (CDL) restraints added in 917.1 milliseconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 24 sheets defined 27.5% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.551A pdb=" N ILE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.532A pdb=" N GLY A 117 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'B' and resid 60 through 69 Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.551A pdb=" N ILE B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.531A pdb=" N GLY B 117 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'D' and resid 60 through 69 Processing helix chain 'D' and resid 81 through 95 removed outlier: 3.551A pdb=" N ILE D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.531A pdb=" N GLY D 117 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'E' and resid 60 through 69 Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.551A pdb=" N ILE E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.531A pdb=" N GLY E 117 " --> pdb=" O GLU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 152 through 154 No H-bonds generated for 'chain 'E' and resid 152 through 154' Processing helix chain 'F' and resid 60 through 69 Processing helix chain 'F' and resid 81 through 95 removed outlier: 3.551A pdb=" N ILE F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 118 removed outlier: 3.532A pdb=" N GLY F 117 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 152 through 154 No H-bonds generated for 'chain 'F' and resid 152 through 154' Processing helix chain 'G' and resid 60 through 69 Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.550A pdb=" N ILE G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.532A pdb=" N GLY G 117 " --> pdb=" O GLU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 140 Processing helix chain 'G' and resid 152 through 154 No H-bonds generated for 'chain 'G' and resid 152 through 154' Processing helix chain 'H' and resid 60 through 69 Processing helix chain 'H' and resid 81 through 95 removed outlier: 3.551A pdb=" N ILE H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 removed outlier: 3.532A pdb=" N GLY H 117 " --> pdb=" O GLU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 152 through 154 No H-bonds generated for 'chain 'H' and resid 152 through 154' Processing helix chain 'I' and resid 60 through 69 Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.550A pdb=" N ILE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 118 removed outlier: 3.531A pdb=" N GLY I 117 " --> pdb=" O GLU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 140 Processing helix chain 'I' and resid 152 through 154 No H-bonds generated for 'chain 'I' and resid 152 through 154' Processing helix chain 'J' and resid 60 through 69 Processing helix chain 'J' and resid 81 through 95 removed outlier: 3.551A pdb=" N ILE J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 118 removed outlier: 3.531A pdb=" N GLY J 117 " --> pdb=" O GLU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 140 Processing helix chain 'J' and resid 152 through 154 No H-bonds generated for 'chain 'J' and resid 152 through 154' Processing helix chain 'K' and resid 60 through 69 Processing helix chain 'K' and resid 81 through 95 removed outlier: 3.550A pdb=" N ILE K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 118 removed outlier: 3.532A pdb=" N GLY K 117 " --> pdb=" O GLU K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 140 Processing helix chain 'K' and resid 152 through 154 No H-bonds generated for 'chain 'K' and resid 152 through 154' Processing helix chain 'L' and resid 60 through 69 Processing helix chain 'L' and resid 81 through 95 removed outlier: 3.550A pdb=" N ILE L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 118 removed outlier: 3.532A pdb=" N GLY L 117 " --> pdb=" O GLU L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 Processing helix chain 'L' and resid 152 through 154 No H-bonds generated for 'chain 'L' and resid 152 through 154' Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 81 through 95 removed outlier: 3.551A pdb=" N ILE C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 removed outlier: 3.532A pdb=" N GLY C 117 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.324A pdb=" N SER A 57 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 167 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.518A pdb=" N ILE A 104 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA A 147 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 47 removed outlier: 6.325A pdb=" N SER B 57 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU B 167 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE B 104 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA B 147 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 45 through 47 removed outlier: 6.325A pdb=" N SER D 57 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU D 167 " --> pdb=" O SER D 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE D 104 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA D 147 " --> pdb=" O ILE D 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 45 through 47 removed outlier: 6.325A pdb=" N SER E 57 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU E 167 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE E 104 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA E 147 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 45 through 47 removed outlier: 6.325A pdb=" N SER F 57 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU F 167 " --> pdb=" O SER F 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE F 104 " --> pdb=" O ALA F 147 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA F 147 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 45 through 47 removed outlier: 6.325A pdb=" N SER G 57 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU G 167 " --> pdb=" O SER G 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE G 104 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA G 147 " --> pdb=" O ILE G 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 45 through 47 removed outlier: 6.325A pdb=" N SER H 57 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU H 167 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE H 104 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA H 147 " --> pdb=" O ILE H 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 45 through 47 removed outlier: 6.325A pdb=" N SER I 57 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU I 167 " --> pdb=" O SER I 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE I 104 " --> pdb=" O ALA I 147 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA I 147 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 45 through 47 removed outlier: 6.326A pdb=" N SER J 57 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU J 167 " --> pdb=" O SER J 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE J 104 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA J 147 " --> pdb=" O ILE J 104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 45 through 47 removed outlier: 6.325A pdb=" N SER K 57 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU K 167 " --> pdb=" O SER K 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 121 through 122 removed outlier: 3.520A pdb=" N ILE K 104 " --> pdb=" O ALA K 147 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA K 147 " --> pdb=" O ILE K 104 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 45 through 47 removed outlier: 6.325A pdb=" N SER L 57 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU L 167 " --> pdb=" O SER L 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE L 104 " --> pdb=" O ALA L 147 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA L 147 " --> pdb=" O ILE L 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 6.326A pdb=" N SER C 57 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU C 167 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 121 through 122 removed outlier: 3.519A pdb=" N ILE C 104 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA C 147 " --> pdb=" O ILE C 104 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1116 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: 1.99 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4080 1.35 - 1.46: 3733 1.46 - 1.58: 5543 1.58 - 1.70: 0 1.70 - 1.81: 96 Bond restraints: 13452 Sorted by residual: bond pdb=" CB PRO F 143 " pdb=" CG PRO F 143 " ideal model delta sigma weight residual 1.492 1.526 -0.034 5.00e-02 4.00e+02 4.53e-01 bond pdb=" CB PRO D 143 " pdb=" CG PRO D 143 " ideal model delta sigma weight residual 1.492 1.526 -0.034 5.00e-02 4.00e+02 4.49e-01 bond pdb=" CB PRO I 143 " pdb=" CG PRO I 143 " ideal model delta sigma weight residual 1.492 1.525 -0.033 5.00e-02 4.00e+02 4.46e-01 bond pdb=" CB PRO L 143 " pdb=" CG PRO L 143 " ideal model delta sigma weight residual 1.492 1.525 -0.033 5.00e-02 4.00e+02 4.46e-01 bond pdb=" CB PRO B 143 " pdb=" CG PRO B 143 " ideal model delta sigma weight residual 1.492 1.525 -0.033 5.00e-02 4.00e+02 4.43e-01 ... (remaining 13447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.65: 16283 0.65 - 1.29: 1696 1.29 - 1.94: 157 1.94 - 2.58: 104 2.58 - 3.23: 96 Bond angle restraints: 18336 Sorted by residual: angle pdb=" CA LYS I 42 " pdb=" CB LYS I 42 " pdb=" CG LYS I 42 " ideal model delta sigma weight residual 114.10 110.87 3.23 2.00e+00 2.50e-01 2.60e+00 angle pdb=" CA LYS B 42 " pdb=" CB LYS B 42 " pdb=" CG LYS B 42 " ideal model delta sigma weight residual 114.10 110.88 3.22 2.00e+00 2.50e-01 2.59e+00 angle pdb=" CA LYS H 42 " pdb=" CB LYS H 42 " pdb=" CG LYS H 42 " ideal model delta sigma weight residual 114.10 110.88 3.22 2.00e+00 2.50e-01 2.59e+00 angle pdb=" CA LYS J 42 " pdb=" CB LYS J 42 " pdb=" CG LYS J 42 " ideal model delta sigma weight residual 114.10 110.89 3.21 2.00e+00 2.50e-01 2.57e+00 angle pdb=" CA LYS G 42 " pdb=" CB LYS G 42 " pdb=" CG LYS G 42 " ideal model delta sigma weight residual 114.10 110.89 3.21 2.00e+00 2.50e-01 2.57e+00 ... (remaining 18331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.61: 6493 11.61 - 23.21: 795 23.21 - 34.82: 368 34.82 - 46.43: 85 46.43 - 58.04: 167 Dihedral angle restraints: 7908 sinusoidal: 3072 harmonic: 4836 Sorted by residual: dihedral pdb=" CA LYS J 42 " pdb=" C LYS J 42 " pdb=" N GLY J 43 " pdb=" CA GLY J 43 " ideal model delta harmonic sigma weight residual -180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LYS A 42 " pdb=" C LYS A 42 " pdb=" N GLY A 43 " pdb=" CA GLY A 43 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LYS E 42 " pdb=" C LYS E 42 " pdb=" N GLY E 43 " pdb=" CA GLY E 43 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 7905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 968 0.024 - 0.049: 569 0.049 - 0.073: 216 0.073 - 0.097: 63 0.097 - 0.122: 56 Chirality restraints: 1872 Sorted by residual: chirality pdb=" CA ILE K 140 " pdb=" N ILE K 140 " pdb=" C ILE K 140 " pdb=" CB ILE K 140 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA ILE E 140 " pdb=" N ILE E 140 " pdb=" C ILE E 140 " pdb=" CB ILE E 140 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE B 140 " pdb=" N ILE B 140 " pdb=" C ILE B 140 " pdb=" CB ILE B 140 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 1869 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP G 160 " 0.003 2.00e-02 2.50e+03 6.35e-03 4.03e-01 pdb=" C ASP G 160 " -0.011 2.00e-02 2.50e+03 pdb=" O ASP G 160 " 0.004 2.00e-02 2.50e+03 pdb=" N TYR G 161 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 166 " -0.054 9.50e-02 1.11e+02 2.42e-02 3.98e-01 pdb=" NE ARG H 166 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG H 166 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG H 166 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 166 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 166 " -0.053 9.50e-02 1.11e+02 2.38e-02 3.98e-01 pdb=" NE ARG G 166 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG G 166 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 166 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 166 " -0.003 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5151 2.88 - 3.38: 11305 3.38 - 3.89: 24106 3.89 - 4.39: 27937 4.39 - 4.90: 45253 Nonbonded interactions: 113752 Sorted by model distance: nonbonded pdb=" OG SER K 124 " pdb=" OD1 ASP K 126 " model vdw 2.370 3.040 nonbonded pdb=" OG SER G 124 " pdb=" OD1 ASP G 126 " model vdw 2.370 3.040 nonbonded pdb=" OG SER E 124 " pdb=" OD1 ASP E 126 " model vdw 2.370 3.040 nonbonded pdb=" OG SER A 124 " pdb=" OD1 ASP A 126 " model vdw 2.370 3.040 nonbonded pdb=" OG SER J 124 " pdb=" OD1 ASP J 126 " model vdw 2.371 3.040 ... (remaining 113747 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.490 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.002 0.034 13488 Z= 0.087 Angle : 0.462 3.227 18408 Z= 0.252 Chirality : 0.038 0.122 1872 Planarity : 0.003 0.024 2340 Dihedral : 15.680 58.037 4728 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 19.17 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1644 helix: 2.94 (0.29), residues: 300 sheet: 1.57 (0.32), residues: 216 loop : 0.33 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 166 TYR 0.006 0.001 TYR L 101 PHE 0.003 0.001 PHE E 55 TRP 0.009 0.001 TRP J 103 HIS 0.002 0.001 HIS I 107 Details of bonding type rmsd covalent geometry : bond 0.00200 (13452) covalent geometry : angle 0.46183 (18336) SS BOND : bond 0.00115 ( 36) SS BOND : angle 0.54354 ( 72) hydrogen bonds : bond 0.22635 ( 468) hydrogen bonds : angle 6.41658 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.477 Fit side-chains REVERT: B 166 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7769 (mtp85) REVERT: D 111 GLN cc_start: 0.8365 (mt0) cc_final: 0.7805 (mt0) REVERT: G 135 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7778 (ptm160) REVERT: L 135 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7769 (ptm160) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.8472 time to fit residues: 207.1304 Evaluate side-chains 205 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN E 111 GLN E 116 ASN E 162 ASN F 111 GLN G 111 GLN H 111 GLN H 162 ASN I 111 GLN I 162 ASN J 111 GLN K 111 GLN L 111 GLN L 162 ASN C 111 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.095516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.069366 restraints weight = 37512.867| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.89 r_work: 0.2560 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2423 r_free = 0.2423 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 = 0.2423 r_free = 0.2423 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13488 Z= 0.177 Angle : 0.550 3.735 18408 Z= 0.303 Chirality : 0.042 0.109 1872 Planarity : 0.004 0.035 2340 Dihedral : 5.048 15.932 1848 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.46 % Allowed : 18.19 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.21), residues: 1644 helix: 2.78 (0.32), residues: 312 sheet: 1.89 (0.33), residues: 192 loop : 0.38 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 166 TYR 0.013 0.001 TYR K 101 PHE 0.010 0.002 PHE E 173 TRP 0.007 0.001 TRP G 158 HIS 0.003 0.002 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00433 (13452) covalent geometry : angle 0.54767 (18336) SS BOND : bond 0.00145 ( 36) SS BOND : angle 0.93366 ( 72) hydrogen bonds : bond 0.05998 ( 468) hydrogen bonds : angle 4.09635 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.481 Fit side-chains REVERT: A 151 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8487 (ttm-80) REVERT: B 166 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8228 (mtp85) REVERT: D 42 LYS cc_start: 0.8627 (tttm) cc_final: 0.8150 (mptt) REVERT: D 111 GLN cc_start: 0.8467 (mt0) cc_final: 0.7914 (mt0) REVERT: F 39 ARG cc_start: 0.8043 (ttt180) cc_final: 0.6370 (mpp80) REVERT: F 42 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8370 (mptp) REVERT: G 135 ARG cc_start: 0.8424 (ptm160) cc_final: 0.8127 (ptm160) REVERT: G 175 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.5928 (t70) REVERT: H 42 LYS cc_start: 0.8700 (tttm) cc_final: 0.8129 (mptp) REVERT: I 135 ARG cc_start: 0.8559 (ptm160) cc_final: 0.8146 (ptm160) REVERT: I 151 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8456 (ttm-80) REVERT: I 175 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6080 (t70) REVERT: J 42 LYS cc_start: 0.8810 (tppt) cc_final: 0.8562 (mptp) outliers start: 21 outliers final: 0 residues processed: 223 average time/residue: 0.9604 time to fit residues: 225.7134 Evaluate side-chains 198 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain I residue 175 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 162 ASN B 111 GLN B 162 ASN E 111 GLN E 164 ASN F 111 GLN G 111 GLN H 111 GLN H 162 ASN I 111 GLN I 162 ASN J 111 GLN K 111 GLN C 111 GLN C 162 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.070767 restraints weight = 30410.904| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.62 r_work: 0.2589 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2455 r_free = 0.2455 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2455 r_free = 0.2455 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13488 Z= 0.137 Angle : 0.508 3.375 18408 Z= 0.279 Chirality : 0.041 0.116 1872 Planarity : 0.003 0.026 2340 Dihedral : 4.809 14.552 1848 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.60 % Allowed : 18.12 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1644 helix: 2.74 (0.31), residues: 312 sheet: 1.65 (0.32), residues: 192 loop : 0.39 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.009 0.001 TYR C 101 PHE 0.009 0.001 PHE B 173 TRP 0.005 0.001 TRP K 103 HIS 0.004 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00341 (13452) covalent geometry : angle 0.50642 (18336) SS BOND : bond 0.00153 ( 36) SS BOND : angle 0.80209 ( 72) hydrogen bonds : bond 0.05136 ( 468) hydrogen bonds : angle 3.86722 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.479 Fit side-chains REVERT: A 151 ARG cc_start: 0.8804 (ttm-80) cc_final: 0.8561 (ttm-80) REVERT: B 166 ARG cc_start: 0.8567 (mtp180) cc_final: 0.8234 (mtp85) REVERT: B 175 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6016 (t70) REVERT: D 42 LYS cc_start: 0.8680 (tttm) cc_final: 0.8239 (mptt) REVERT: D 111 GLN cc_start: 0.8425 (mt0) cc_final: 0.7883 (mt0) REVERT: D 175 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.5916 (t70) REVERT: E 135 ARG cc_start: 0.8434 (ptm160) cc_final: 0.8088 (ptm160) REVERT: F 39 ARG cc_start: 0.8036 (ttt180) cc_final: 0.5883 (mpp80) REVERT: F 175 ASP cc_start: 0.6480 (OUTLIER) cc_final: 0.5817 (t70) REVERT: G 162 ASN cc_start: 0.8874 (t0) cc_final: 0.8573 (t0) REVERT: H 42 LYS cc_start: 0.8660 (tttm) cc_final: 0.8242 (mmtp) REVERT: H 175 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6295 (t70) REVERT: I 135 ARG cc_start: 0.8578 (ptm160) cc_final: 0.8231 (ptm160) REVERT: I 151 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8488 (ttm-80) REVERT: K 175 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6203 (t70) REVERT: L 39 ARG cc_start: 0.8265 (ttt180) cc_final: 0.7707 (ttt-90) REVERT: L 175 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6605 (t70) outliers start: 23 outliers final: 4 residues processed: 225 average time/residue: 0.9506 time to fit residues: 225.2746 Evaluate side-chains 208 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 175 ASP Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain C residue 38 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 77 optimal weight: 0.0870 chunk 126 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 49 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 162 ASN B 111 GLN B 162 ASN E 111 GLN E 164 ASN F 111 GLN F 164 ASN G 111 GLN H 111 GLN H 162 ASN I 111 GLN I 162 ASN J 111 GLN J 164 ASN K 111 GLN L 162 ASN C 111 GLN C 162 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.072749 restraints weight = 45854.816| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.10 r_work: 0.2616 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 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 = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13488 Z= 0.092 Angle : 0.454 3.255 18408 Z= 0.248 Chirality : 0.039 0.124 1872 Planarity : 0.003 0.025 2340 Dihedral : 4.400 13.186 1848 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.83 % Allowed : 18.82 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1644 helix: 2.99 (0.31), residues: 312 sheet: 2.08 (0.39), residues: 120 loop : 0.34 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 135 TYR 0.006 0.001 TYR J 101 PHE 0.006 0.001 PHE B 173 TRP 0.006 0.001 TRP C 133 HIS 0.002 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00223 (13452) covalent geometry : angle 0.45266 (18336) SS BOND : bond 0.00123 ( 36) SS BOND : angle 0.70181 ( 72) hydrogen bonds : bond 0.04008 ( 468) hydrogen bonds : angle 3.76796 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.380 Fit side-chains REVERT: A 151 ARG cc_start: 0.8812 (ttm-80) cc_final: 0.8582 (ttm-80) REVERT: B 166 ARG cc_start: 0.8644 (mtp180) cc_final: 0.8308 (mtp85) REVERT: D 42 LYS cc_start: 0.8726 (tttm) cc_final: 0.8352 (mptt) REVERT: D 111 GLN cc_start: 0.8455 (mt0) cc_final: 0.7912 (mt0) REVERT: D 145 HIS cc_start: 0.8009 (m-70) cc_final: 0.7787 (m90) REVERT: F 39 ARG cc_start: 0.8050 (ttt180) cc_final: 0.6300 (mpp80) REVERT: F 136 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7560 (m-40) REVERT: H 42 LYS cc_start: 0.8711 (tttm) cc_final: 0.8320 (mmtp) REVERT: I 135 ARG cc_start: 0.8563 (ptm160) cc_final: 0.8196 (ptm160) REVERT: I 151 ARG cc_start: 0.8769 (ttm-80) cc_final: 0.8524 (ttm-80) REVERT: K 166 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8390 (mtp85) REVERT: L 39 ARG cc_start: 0.8263 (ttt180) cc_final: 0.7947 (ttt-90) REVERT: L 42 LYS cc_start: 0.7348 (pptt) cc_final: 0.6552 (mmtp) REVERT: L 166 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8249 (mtp85) REVERT: C 39 ARG cc_start: 0.8426 (ttt180) cc_final: 0.7905 (ttt-90) outliers start: 12 outliers final: 3 residues processed: 218 average time/residue: 1.0050 time to fit residues: 230.1682 Evaluate side-chains 204 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 200 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain C residue 38 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 141 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 162 ASN B 111 GLN D 162 ASN E 111 GLN E 164 ASN F 111 GLN G 111 GLN H 111 GLN I 111 GLN J 111 GLN J 162 ASN J 164 ASN K 111 GLN C 111 GLN C 162 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.094759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.069559 restraints weight = 33453.737| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.65 r_work: 0.2543 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2404 r_free = 0.2404 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2404 r_free = 0.2404 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 13488 Z= 0.234 Angle : 0.581 4.468 18408 Z= 0.316 Chirality : 0.044 0.122 1872 Planarity : 0.004 0.030 2340 Dihedral : 5.113 15.780 1848 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.39 % Allowed : 18.40 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1644 helix: 2.60 (0.31), residues: 312 sheet: 1.06 (0.33), residues: 192 loop : 0.35 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 71 TYR 0.015 0.002 TYR K 101 PHE 0.013 0.002 PHE E 173 TRP 0.009 0.001 TRP G 158 HIS 0.005 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00575 (13452) covalent geometry : angle 0.57934 (18336) SS BOND : bond 0.00266 ( 36) SS BOND : angle 0.91972 ( 72) hydrogen bonds : bond 0.05496 ( 468) hydrogen bonds : angle 4.02533 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: B 166 ARG cc_start: 0.8601 (mtp-110) cc_final: 0.8245 (mtp85) REVERT: B 175 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.5925 (t70) REVERT: D 42 LYS cc_start: 0.8723 (tttm) cc_final: 0.8376 (mptt) REVERT: D 111 GLN cc_start: 0.8465 (mt0) cc_final: 0.7929 (mt0) REVERT: D 175 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.5927 (t70) REVERT: E 135 ARG cc_start: 0.8472 (ptm160) cc_final: 0.8219 (ptm160) REVERT: F 39 ARG cc_start: 0.8072 (ttt180) cc_final: 0.5911 (mpp80) REVERT: F 162 ASN cc_start: 0.8795 (t0) cc_final: 0.8586 (t0) REVERT: F 175 ASP cc_start: 0.6590 (OUTLIER) cc_final: 0.5922 (t70) REVERT: G 162 ASN cc_start: 0.8941 (t0) cc_final: 0.8713 (t0) REVERT: G 175 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6025 (t70) REVERT: H 42 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8373 (mmtp) REVERT: H 175 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6354 (t70) REVERT: I 135 ARG cc_start: 0.8665 (ptm160) cc_final: 0.8315 (ptm160) REVERT: I 175 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.5963 (t70) REVERT: K 175 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6290 (t70) REVERT: L 39 ARG cc_start: 0.8273 (ttt180) cc_final: 0.7972 (ttt-90) REVERT: C 175 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6078 (t70) outliers start: 20 outliers final: 3 residues processed: 217 average time/residue: 0.9909 time to fit residues: 226.1651 Evaluate side-chains 205 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 175 ASP Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain C residue 175 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 149 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 63 optimal weight: 0.0870 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 162 ASN E 111 GLN E 164 ASN F 111 GLN G 111 GLN H 111 GLN H 162 ASN I 111 GLN I 162 ASN J 111 GLN J 164 ASN K 111 GLN L 162 ASN C 111 GLN C 162 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.070947 restraints weight = 40201.780| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.94 r_work: 0.2584 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13488 Z= 0.105 Angle : 0.476 3.292 18408 Z= 0.260 Chirality : 0.040 0.121 1872 Planarity : 0.003 0.025 2340 Dihedral : 4.651 13.967 1848 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.69 % Allowed : 19.24 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.21), residues: 1644 helix: 2.90 (0.31), residues: 312 sheet: 1.68 (0.38), residues: 120 loop : 0.32 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.007 0.001 TYR F 101 PHE 0.006 0.001 PHE J 173 TRP 0.006 0.001 TRP D 133 HIS 0.003 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00257 (13452) covalent geometry : angle 0.47508 (18336) SS BOND : bond 0.00128 ( 36) SS BOND : angle 0.72183 ( 72) hydrogen bonds : bond 0.04228 ( 468) hydrogen bonds : angle 3.90473 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 0.542 Fit side-chains REVERT: B 166 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8272 (mtp85) REVERT: D 42 LYS cc_start: 0.8774 (tttm) cc_final: 0.8350 (mptt) REVERT: D 111 GLN cc_start: 0.8443 (mt0) cc_final: 0.7897 (mt0) REVERT: E 135 ARG cc_start: 0.8495 (ptm160) cc_final: 0.8234 (ptm160) REVERT: F 39 ARG cc_start: 0.8075 (ttt180) cc_final: 0.6316 (mpp80) REVERT: F 136 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7498 (m-40) REVERT: H 42 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8361 (mmtp) REVERT: I 135 ARG cc_start: 0.8592 (ptm160) cc_final: 0.8269 (ptm160) REVERT: K 175 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6186 (t70) REVERT: L 39 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7350 (ttt-90) REVERT: L 175 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6300 (t70) REVERT: C 39 ARG cc_start: 0.8377 (ttt180) cc_final: 0.7841 (ttt-90) outliers start: 10 outliers final: 3 residues processed: 207 average time/residue: 1.0368 time to fit residues: 225.4585 Evaluate side-chains 203 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 175 ASP Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 118 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 162 ASN B 111 GLN B 162 ASN D 164 ASN E 111 GLN E 164 ASN F 111 GLN G 111 GLN H 111 GLN H 162 ASN I 111 GLN I 162 ASN J 111 GLN J 162 ASN J 164 ASN K 111 GLN L 162 ASN C 111 GLN C 162 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.095326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.069614 restraints weight = 37652.343| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.87 r_work: 0.2560 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13488 Z= 0.148 Angle : 0.512 3.436 18408 Z= 0.279 Chirality : 0.041 0.121 1872 Planarity : 0.004 0.026 2340 Dihedral : 4.821 14.732 1848 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.04 % Allowed : 19.17 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1644 helix: 2.82 (0.31), residues: 312 sheet: 1.65 (0.38), residues: 120 loop : 0.30 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.010 0.001 TYR K 101 PHE 0.009 0.002 PHE J 173 TRP 0.006 0.001 TRP G 158 HIS 0.003 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00366 (13452) covalent geometry : angle 0.51084 (18336) SS BOND : bond 0.00161 ( 36) SS BOND : angle 0.76221 ( 72) hydrogen bonds : bond 0.04623 ( 468) hydrogen bonds : angle 3.94387 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.411 Fit side-chains REVERT: B 166 ARG cc_start: 0.8606 (mtp-110) cc_final: 0.8268 (mtp85) REVERT: D 42 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8393 (mptt) REVERT: D 111 GLN cc_start: 0.8439 (mt0) cc_final: 0.7906 (mt0) REVERT: E 135 ARG cc_start: 0.8440 (ptm160) cc_final: 0.8183 (ptm160) REVERT: F 39 ARG cc_start: 0.8065 (ttt180) cc_final: 0.6315 (mpp80) REVERT: H 42 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8367 (mmtp) REVERT: H 175 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6368 (t70) REVERT: I 135 ARG cc_start: 0.8593 (ptm160) cc_final: 0.8260 (ptm160) REVERT: I 175 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.5796 (t70) REVERT: K 175 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6197 (t70) REVERT: L 39 ARG cc_start: 0.8239 (ttt180) cc_final: 0.7397 (ttt-90) REVERT: L 175 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6307 (t70) REVERT: C 175 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.5982 (t70) outliers start: 15 outliers final: 4 residues processed: 209 average time/residue: 0.9903 time to fit residues: 217.7804 Evaluate side-chains 205 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 175 ASP Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 175 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 chunk 9 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 162 ASN B 111 GLN B 162 ASN E 111 GLN E 164 ASN F 111 GLN G 111 GLN G 162 ASN H 111 GLN H 162 ASN I 111 GLN I 162 ASN J 111 GLN J 164 ASN K 111 GLN L 162 ASN C 111 GLN C 162 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.070177 restraints weight = 37035.644| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.79 r_work: 0.2552 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2423 r_free = 0.2423 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2423 r_free = 0.2423 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13488 Z= 0.172 Angle : 0.537 3.781 18408 Z= 0.292 Chirality : 0.042 0.121 1872 Planarity : 0.004 0.026 2340 Dihedral : 4.990 15.273 1848 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.97 % Allowed : 19.17 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1644 helix: 2.69 (0.31), residues: 312 sheet: 1.64 (0.39), residues: 120 loop : 0.28 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 71 TYR 0.012 0.002 TYR K 101 PHE 0.010 0.002 PHE B 173 TRP 0.007 0.001 TRP G 158 HIS 0.003 0.002 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00425 (13452) covalent geometry : angle 0.53529 (18336) SS BOND : bond 0.00196 ( 36) SS BOND : angle 0.80853 ( 72) hydrogen bonds : bond 0.04876 ( 468) hydrogen bonds : angle 4.01536 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.524 Fit side-chains REVERT: B 166 ARG cc_start: 0.8620 (mtp-110) cc_final: 0.8287 (mtp85) REVERT: B 175 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.5883 (t70) REVERT: D 42 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8431 (mptt) REVERT: D 111 GLN cc_start: 0.8466 (mt0) cc_final: 0.7931 (mt0) REVERT: D 175 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.5853 (t70) REVERT: E 135 ARG cc_start: 0.8456 (ptm160) cc_final: 0.8207 (ptm160) REVERT: F 39 ARG cc_start: 0.8129 (ttt180) cc_final: 0.6432 (mpp80) REVERT: G 175 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.5964 (t70) REVERT: H 42 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8413 (mmtp) REVERT: H 175 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6391 (t70) REVERT: I 135 ARG cc_start: 0.8609 (ptm160) cc_final: 0.8288 (ptm160) REVERT: I 175 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.5875 (t70) REVERT: K 175 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6229 (t70) REVERT: L 39 ARG cc_start: 0.8265 (ttt180) cc_final: 0.7443 (ttt-90) REVERT: L 118 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7495 (mm-30) REVERT: L 175 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6144 (t70) REVERT: C 175 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6005 (t70) outliers start: 14 outliers final: 4 residues processed: 207 average time/residue: 1.0181 time to fit residues: 221.4495 Evaluate side-chains 205 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 175 ASP Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 175 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 140 optimal weight: 0.0050 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 162 ASN B 111 GLN B 162 ASN E 111 GLN E 164 ASN F 111 GLN G 111 GLN H 111 GLN H 162 ASN I 111 GLN I 162 ASN J 111 GLN J 164 ASN K 111 GLN L 162 ASN C 111 GLN C 162 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.071708 restraints weight = 33903.405| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.75 r_work: 0.2602 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 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 = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13488 Z= 0.102 Angle : 0.473 3.321 18408 Z= 0.258 Chirality : 0.039 0.123 1872 Planarity : 0.003 0.027 2340 Dihedral : 4.614 13.994 1848 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.90 % Allowed : 19.31 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1644 helix: 2.97 (0.31), residues: 312 sheet: 1.51 (0.38), residues: 120 loop : 0.32 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.007 0.001 TYR K 101 PHE 0.006 0.001 PHE G 173 TRP 0.006 0.001 TRP A 103 HIS 0.003 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00252 (13452) covalent geometry : angle 0.47183 (18336) SS BOND : bond 0.00130 ( 36) SS BOND : angle 0.72508 ( 72) hydrogen bonds : bond 0.04061 ( 468) hydrogen bonds : angle 3.93467 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.513 Fit side-chains REVERT: B 166 ARG cc_start: 0.8583 (mtp-110) cc_final: 0.8249 (mtp85) REVERT: B 175 ASP cc_start: 0.6447 (OUTLIER) cc_final: 0.5893 (t70) REVERT: D 42 LYS cc_start: 0.8729 (tttm) cc_final: 0.8342 (mptt) REVERT: D 111 GLN cc_start: 0.8442 (mt0) cc_final: 0.7895 (mt0) REVERT: D 175 ASP cc_start: 0.6538 (OUTLIER) cc_final: 0.5843 (t70) REVERT: E 118 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: E 135 ARG cc_start: 0.8487 (ptm160) cc_final: 0.8231 (ptm160) REVERT: F 39 ARG cc_start: 0.8056 (ttt180) cc_final: 0.6303 (mpp80) REVERT: H 42 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8374 (mmtp) REVERT: H 175 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6367 (t70) REVERT: I 135 ARG cc_start: 0.8581 (ptm160) cc_final: 0.8264 (ptm160) REVERT: K 166 ARG cc_start: 0.8680 (mtp-110) cc_final: 0.8399 (mtp85) REVERT: K 175 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6164 (t70) REVERT: L 39 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7394 (ttt-90) REVERT: L 118 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7427 (mm-30) REVERT: L 166 ARG cc_start: 0.8629 (mtp-110) cc_final: 0.8205 (mtp85) REVERT: L 175 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6274 (t70) REVERT: C 175 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.5975 (t70) outliers start: 13 outliers final: 3 residues processed: 212 average time/residue: 1.0244 time to fit residues: 228.1202 Evaluate side-chains 210 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 175 ASP Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 175 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 142 optimal weight: 0.4980 chunk 50 optimal weight: 0.0060 chunk 99 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 162 ASN B 111 GLN B 162 ASN E 111 GLN E 164 ASN G 111 GLN G 164 ASN H 111 GLN I 111 GLN I 162 ASN J 111 GLN J 162 ASN J 164 ASN K 111 GLN C 111 GLN C 162 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.095669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.069747 restraints weight = 40620.966| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.97 r_work: 0.2563 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13488 Z= 0.135 Angle : 0.503 3.346 18408 Z= 0.273 Chirality : 0.040 0.120 1872 Planarity : 0.003 0.027 2340 Dihedral : 4.762 14.335 1848 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.97 % Allowed : 19.38 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1644 helix: 2.88 (0.31), residues: 312 sheet: 1.52 (0.38), residues: 120 loop : 0.32 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 135 TYR 0.009 0.001 TYR A 101 PHE 0.008 0.002 PHE J 173 TRP 0.005 0.001 TRP C 103 HIS 0.003 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00334 (13452) covalent geometry : angle 0.50147 (18336) SS BOND : bond 0.00151 ( 36) SS BOND : angle 0.74561 ( 72) hydrogen bonds : bond 0.04424 ( 468) hydrogen bonds : angle 3.94397 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.506 Fit side-chains REVERT: B 166 ARG cc_start: 0.8603 (mtp-110) cc_final: 0.8269 (mtp85) REVERT: B 175 ASP cc_start: 0.6471 (OUTLIER) cc_final: 0.5919 (t70) REVERT: D 42 LYS cc_start: 0.8759 (tttm) cc_final: 0.8351 (mptt) REVERT: D 111 GLN cc_start: 0.8450 (mt0) cc_final: 0.7906 (mt0) REVERT: D 175 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.5883 (t70) REVERT: E 135 ARG cc_start: 0.8490 (ptm160) cc_final: 0.8240 (ptm160) REVERT: F 39 ARG cc_start: 0.8076 (ttt180) cc_final: 0.6298 (mpp80) REVERT: G 175 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.5982 (t70) REVERT: H 42 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8379 (mmtp) REVERT: H 175 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6405 (t70) REVERT: I 135 ARG cc_start: 0.8586 (ptm160) cc_final: 0.8270 (ptm160) REVERT: K 166 ARG cc_start: 0.8714 (mtp-110) cc_final: 0.8427 (mtp85) REVERT: K 175 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6226 (t70) REVERT: L 39 ARG cc_start: 0.8238 (ttt180) cc_final: 0.7407 (ttt-90) REVERT: L 118 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7604 (mm-30) REVERT: L 166 ARG cc_start: 0.8663 (mtp-110) cc_final: 0.8233 (mtp85) REVERT: L 175 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6356 (t70) REVERT: C 39 ARG cc_start: 0.8373 (ttt180) cc_final: 0.7434 (ttt-90) REVERT: C 175 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.6006 (t70) outliers start: 14 outliers final: 2 residues processed: 210 average time/residue: 1.0039 time to fit residues: 221.3994 Evaluate side-chains 206 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 175 ASP Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain C residue 175 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 9 optimal weight: 0.0670 chunk 34 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 162 ASN B 111 GLN B 162 ASN E 111 GLN E 164 ASN G 111 GLN G 164 ASN H 111 GLN H 162 ASN I 111 GLN I 162 ASN J 111 GLN J 164 ASN K 111 GLN C 111 GLN C 162 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.069545 restraints weight = 47034.520| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.13 r_work: 0.2554 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13488 Z= 0.131 Angle : 0.500 3.346 18408 Z= 0.272 Chirality : 0.040 0.121 1872 Planarity : 0.003 0.028 2340 Dihedral : 4.752 14.210 1848 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.83 % Allowed : 19.44 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1644 helix: 2.89 (0.31), residues: 312 sheet: 1.48 (0.38), residues: 120 loop : 0.32 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 135 TYR 0.009 0.001 TYR K 101 PHE 0.008 0.001 PHE B 173 TRP 0.005 0.001 TRP D 103 HIS 0.003 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00324 (13452) covalent geometry : angle 0.49840 (18336) SS BOND : bond 0.00149 ( 36) SS BOND : angle 0.74500 ( 72) hydrogen bonds : bond 0.04376 ( 468) hydrogen bonds : angle 3.94874 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6526.59 seconds wall clock time: 111 minutes 15.58 seconds (6675.58 seconds total)