Starting phenix.real_space_refine on Tue Dec 31 19:06:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stw_25437/12_2024/7stw_25437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stw_25437/12_2024/7stw_25437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stw_25437/12_2024/7stw_25437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stw_25437/12_2024/7stw_25437.map" model { file = "/net/cci-nas-00/data/ceres_data/7stw_25437/12_2024/7stw_25437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stw_25437/12_2024/7stw_25437.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.484 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: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 Zn 12 6.06 5 S 36 5.16 5 C 10632 2.51 5 N 2724 2.21 5 O 3413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16829 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "B" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "C" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "D" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "E" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "F" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "G" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "H" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "I" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "J" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "K" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "L" Number of atoms: 1379 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 170, 1379 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "I" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "J" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "K" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "L" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 9.63, per 1000 atoms: 0.57 Number of scatterers: 16829 At special positions: 0 Unit cell: (108.288, 114.048, 108.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 Fe 12 26.01 S 36 16.00 O 3413 8.00 N 2724 7.00 C 10632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.25 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" ND1 HIS A 66 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 66 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 66 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" ND1 HIS D 66 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 66 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 66 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 66 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 66 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 66 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 66 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 66 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 66 " 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 77 removed outlier: 4.339A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 104 through 131 Processing helix chain 'A' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'B' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR B 38 " --> pdb=" O TYR B 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 104 through 131 Processing helix chain 'B' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'C' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C 38 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 72 - end of helix Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 104 through 131 Processing helix chain 'C' and resid 134 through 160 removed outlier: 3.786A pdb=" N GLU C 147 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'D' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 72 - end of helix Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 131 Processing helix chain 'D' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'E' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 77 removed outlier: 4.337A pdb=" N ALA E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 104 through 131 Processing helix chain 'E' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR F 38 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE F 39 " --> pdb=" O TYR F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 77 removed outlier: 4.337A pdb=" N ALA F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'F' and resid 84 through 90 Processing helix chain 'F' and resid 104 through 131 Processing helix chain 'F' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU F 147 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'G' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR G 38 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE G 39 " --> pdb=" O TYR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 72 - end of helix Processing helix chain 'G' and resid 84 through 90 Processing helix chain 'G' and resid 104 through 131 Processing helix chain 'G' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'H' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE H 39 " --> pdb=" O TYR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU H 54 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 72 - end of helix Processing helix chain 'H' and resid 84 through 90 Processing helix chain 'H' and resid 104 through 131 Processing helix chain 'H' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU H 147 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 182 Processing helix chain 'I' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR I 35 " --> pdb=" O PHE I 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR I 38 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE I 39 " --> pdb=" O TYR I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 4.337A pdb=" N ALA I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU I 54 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 72 - end of helix Processing helix chain 'I' and resid 84 through 90 Processing helix chain 'I' and resid 104 through 131 Processing helix chain 'I' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 182 Processing helix chain 'J' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR J 35 " --> pdb=" O PHE J 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR J 38 " --> pdb=" O TYR J 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE J 39 " --> pdb=" O TYR J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 72 - end of helix Processing helix chain 'J' and resid 84 through 90 Processing helix chain 'J' and resid 104 through 131 Processing helix chain 'J' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU J 147 " --> pdb=" O ALA J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'K' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR K 35 " --> pdb=" O PHE K 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR K 38 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE K 39 " --> pdb=" O TYR K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 77 removed outlier: 4.338A pdb=" N ALA K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 72 - end of helix Processing helix chain 'K' and resid 84 through 90 Processing helix chain 'K' and resid 104 through 131 Processing helix chain 'K' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU K 147 " --> pdb=" O ALA K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 182 Processing helix chain 'L' and resid 15 through 43 removed outlier: 3.770A pdb=" N TYR L 35 " --> pdb=" O PHE L 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR L 38 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE L 39 " --> pdb=" O TYR L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 77 removed outlier: 4.337A pdb=" N ALA L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) Proline residue: L 72 - end of helix Processing helix chain 'L' and resid 84 through 90 Processing helix chain 'L' and resid 104 through 131 Processing helix chain 'L' and resid 134 through 160 removed outlier: 3.787A pdb=" N GLU L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 182 1140 hydrogen bonds defined for protein. 3336 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: 4.97 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5472 1.34 - 1.46: 3763 1.46 - 1.58: 7649 1.58 - 1.70: 0 1.70 - 1.81: 36 Bond restraints: 16920 Sorted by residual: bond pdb=" C GLY B 161 " pdb=" O GLY B 161 " ideal model delta sigma weight residual 1.239 1.233 0.005 7.10e-03 1.98e+04 5.84e-01 bond pdb=" C GLY A 161 " pdb=" O GLY A 161 " ideal model delta sigma weight residual 1.239 1.233 0.005 7.10e-03 1.98e+04 5.42e-01 bond pdb=" C GLY I 161 " pdb=" O GLY I 161 " ideal model delta sigma weight residual 1.239 1.233 0.005 7.10e-03 1.98e+04 5.22e-01 bond pdb=" N PRO A 103 " pdb=" CA PRO A 103 " ideal model delta sigma weight residual 1.479 1.468 0.011 1.56e-02 4.11e+03 4.94e-01 bond pdb=" N PRO J 103 " pdb=" CA PRO J 103 " ideal model delta sigma weight residual 1.479 1.468 0.011 1.56e-02 4.11e+03 4.94e-01 ... (remaining 16915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 21192 0.87 - 1.74: 1457 1.74 - 2.62: 191 2.62 - 3.49: 56 3.49 - 4.36: 24 Bond angle restraints: 22920 Sorted by residual: angle pdb=" C VAL F 178 " pdb=" CA VAL F 178 " pdb=" CB VAL F 178 " ideal model delta sigma weight residual 111.85 109.71 2.14 1.27e+00 6.20e-01 2.84e+00 angle pdb=" C VAL D 178 " pdb=" CA VAL D 178 " pdb=" CB VAL D 178 " ideal model delta sigma weight residual 111.85 109.71 2.14 1.27e+00 6.20e-01 2.83e+00 angle pdb=" C VAL G 178 " pdb=" CA VAL G 178 " pdb=" CB VAL G 178 " ideal model delta sigma weight residual 111.85 109.72 2.13 1.27e+00 6.20e-01 2.81e+00 angle pdb=" C VAL J 178 " pdb=" CA VAL J 178 " pdb=" CB VAL J 178 " ideal model delta sigma weight residual 111.85 109.72 2.13 1.27e+00 6.20e-01 2.80e+00 angle pdb=" C VAL B 178 " pdb=" CA VAL B 178 " pdb=" CB VAL B 178 " ideal model delta sigma weight residual 111.85 109.73 2.12 1.27e+00 6.20e-01 2.80e+00 ... (remaining 22915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.83: 8849 13.83 - 27.66: 955 27.66 - 41.48: 324 41.48 - 55.31: 24 55.31 - 69.14: 36 Dihedral angle restraints: 10188 sinusoidal: 4200 harmonic: 5988 Sorted by residual: dihedral pdb=" CG ARG A 73 " pdb=" CD ARG A 73 " pdb=" NE ARG A 73 " pdb=" CZ ARG A 73 " ideal model delta sinusoidal sigma weight residual 90.00 128.35 -38.35 2 1.50e+01 4.44e-03 8.21e+00 dihedral pdb=" CG ARG K 73 " pdb=" CD ARG K 73 " pdb=" NE ARG K 73 " pdb=" CZ ARG K 73 " ideal model delta sinusoidal sigma weight residual 90.00 128.33 -38.33 2 1.50e+01 4.44e-03 8.21e+00 dihedral pdb=" CG ARG H 73 " pdb=" CD ARG H 73 " pdb=" NE ARG H 73 " pdb=" CZ ARG H 73 " ideal model delta sinusoidal sigma weight residual 90.00 128.33 -38.33 2 1.50e+01 4.44e-03 8.21e+00 ... (remaining 10185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1356 0.026 - 0.051: 800 0.051 - 0.076: 292 0.076 - 0.102: 24 0.102 - 0.127: 36 Chirality restraints: 2508 Sorted by residual: chirality pdb=" CA PRO D 135 " pdb=" N PRO D 135 " pdb=" C PRO D 135 " pdb=" CB PRO D 135 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA PRO H 135 " pdb=" N PRO H 135 " pdb=" C PRO H 135 " pdb=" CB PRO H 135 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA PRO G 135 " pdb=" N PRO G 135 " pdb=" C PRO G 135 " pdb=" CB PRO G 135 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 2505 not shown) Planarity restraints: 2976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 175 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO H 176 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO H 176 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 176 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 175 " 0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO D 176 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 176 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 176 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 175 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO B 176 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " 0.014 5.00e-02 4.00e+02 ... (remaining 2973 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 205 2.54 - 3.13: 11886 3.13 - 3.72: 26237 3.72 - 4.31: 36833 4.31 - 4.90: 59545 Nonbonded interactions: 134706 Sorted by model distance: nonbonded pdb=" OE2 GLU K 148 " pdb="ZN ZN K 201 " model vdw 1.947 2.230 nonbonded pdb=" OE2 GLU C 148 " pdb="ZN ZN C 201 " model vdw 2.011 2.230 nonbonded pdb=" NH1 ARG K 60 " pdb=" O HOH K 301 " model vdw 2.023 3.120 nonbonded pdb=" OE2 GLU F 68 " pdb=" O HOH K 301 " model vdw 2.027 3.040 nonbonded pdb=" OE2 GLU G 148 " pdb="ZN ZN G 201 " model vdw 2.031 2.230 ... (remaining 134701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.920 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.020 16920 Z= 0.158 Angle : 0.500 4.361 22920 Z= 0.305 Chirality : 0.035 0.127 2508 Planarity : 0.004 0.026 2976 Dihedral : 12.966 69.139 6348 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2016 helix: 0.33 (0.12), residues: 1428 sheet: None (None), residues: 0 loop : -0.08 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP L 154 HIS 0.007 0.002 HIS L 151 PHE 0.009 0.002 PHE J 167 TYR 0.012 0.002 TYR L 123 ARG 0.002 0.000 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 625 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASP cc_start: 0.7958 (t70) cc_final: 0.7548 (t0) REVERT: D 150 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6214 (mm-30) REVERT: D 152 GLU cc_start: 0.7904 (tt0) cc_final: 0.7683 (tt0) REVERT: E 116 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8262 (mm-30) REVERT: H 133 LYS cc_start: 0.7832 (mttt) cc_final: 0.7631 (mtpp) REVERT: I 30 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8139 (mm-30) REVERT: J 76 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7977 (mt-10) REVERT: J 134 ASP cc_start: 0.7562 (t0) cc_final: 0.7351 (t0) REVERT: L 25 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8449 (mtpp) REVERT: L 156 GLU cc_start: 0.7270 (tt0) cc_final: 0.7065 (tt0) REVERT: L 158 LEU cc_start: 0.8660 (mt) cc_final: 0.8410 (mt) outliers start: 0 outliers final: 0 residues processed: 625 average time/residue: 2.0440 time to fit residues: 1370.8505 Evaluate side-chains 480 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 119 optimal weight: 30.0000 chunk 185 optimal weight: 30.0000 overall best weight: 11.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN D 128 ASN H 128 ASN L 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16920 Z= 0.322 Angle : 0.722 5.695 22920 Z= 0.414 Chirality : 0.046 0.148 2508 Planarity : 0.006 0.046 2976 Dihedral : 4.292 20.147 2280 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.08 % Allowed : 13.43 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2016 helix: 1.65 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.33 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP K 154 HIS 0.010 0.003 HIS A 146 PHE 0.016 0.003 PHE C 181 TYR 0.025 0.003 TYR K 123 ARG 0.007 0.001 ARG L 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 500 time to evaluate : 1.992 Fit side-chains revert: symmetry clash REVERT: B 84 ASP cc_start: 0.7853 (t70) cc_final: 0.7559 (t0) REVERT: B 128 ASN cc_start: 0.8964 (m-40) cc_final: 0.8642 (m-40) REVERT: B 150 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: D 157 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6836 (tm-30) REVERT: E 125 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: F 52 ILE cc_start: 0.8814 (pt) cc_final: 0.8611 (pt) REVERT: F 83 ARG cc_start: 0.8585 (ttt90) cc_final: 0.8361 (ttt-90) REVERT: H 152 GLU cc_start: 0.7975 (tt0) cc_final: 0.7612 (tt0) REVERT: I 54 GLU cc_start: 0.7271 (tm-30) cc_final: 0.7065 (pp20) REVERT: I 62 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8167 (mm-30) REVERT: I 162 LYS cc_start: 0.7828 (ttpp) cc_final: 0.7610 (tttp) REVERT: J 133 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7659 (mtmt) REVERT: J 150 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: J 180 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8563 (pttp) REVERT: L 25 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8615 (mtpt) REVERT: L 154 TRP cc_start: 0.7336 (OUTLIER) cc_final: 0.6537 (m100) outliers start: 36 outliers final: 10 residues processed: 507 average time/residue: 2.0455 time to fit residues: 1111.8059 Evaluate side-chains 490 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 474 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 165 optimal weight: 30.0000 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 ASN F 107 ASN K 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16920 Z= 0.248 Angle : 0.608 4.661 22920 Z= 0.349 Chirality : 0.041 0.139 2508 Planarity : 0.005 0.031 2976 Dihedral : 4.109 17.577 2280 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.07 % Allowed : 15.51 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.19), residues: 2016 helix: 1.99 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.55 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP J 154 HIS 0.006 0.002 HIS G 66 PHE 0.011 0.002 PHE L 167 TYR 0.021 0.002 TYR I 123 ARG 0.005 0.001 ARG L 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 460 time to evaluate : 1.866 Fit side-chains revert: symmetry clash REVERT: A 154 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.7283 (m100) REVERT: B 84 ASP cc_start: 0.7795 (t70) cc_final: 0.7517 (t0) REVERT: B 150 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: D 152 GLU cc_start: 0.7929 (tt0) cc_final: 0.7648 (tt0) REVERT: E 152 GLU cc_start: 0.8123 (tt0) cc_final: 0.7758 (tt0) REVERT: E 154 TRP cc_start: 0.7528 (OUTLIER) cc_final: 0.6594 (m100) REVERT: F 52 ILE cc_start: 0.8691 (pt) cc_final: 0.8458 (pt) REVERT: F 83 ARG cc_start: 0.8512 (ttt90) cc_final: 0.8307 (ttt-90) REVERT: H 152 GLU cc_start: 0.7960 (tt0) cc_final: 0.7615 (tt0) REVERT: I 54 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6981 (pp20) REVERT: I 83 ARG cc_start: 0.8482 (ttt-90) cc_final: 0.8273 (ttt-90) REVERT: I 114 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: I 162 LYS cc_start: 0.7704 (ttpp) cc_final: 0.7488 (tttp) REVERT: J 150 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8159 (tp30) REVERT: L 128 ASN cc_start: 0.8771 (m-40) cc_final: 0.8529 (m-40) REVERT: L 154 TRP cc_start: 0.7246 (OUTLIER) cc_final: 0.6417 (m100) outliers start: 53 outliers final: 16 residues processed: 472 average time/residue: 2.0585 time to fit residues: 1040.9133 Evaluate side-chains 466 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 444 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 154 TRP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 176 optimal weight: 0.0020 chunk 53 optimal weight: 6.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN C 42 ASN G 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16920 Z= 0.205 Angle : 0.545 4.384 22920 Z= 0.312 Chirality : 0.039 0.126 2508 Planarity : 0.004 0.029 2976 Dihedral : 3.924 14.804 2280 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.49 % Allowed : 16.72 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.19), residues: 2016 helix: 2.25 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.68 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 154 HIS 0.005 0.001 HIS F 146 PHE 0.010 0.002 PHE K 167 TYR 0.018 0.002 TYR I 123 ARG 0.005 0.000 ARG L 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 440 time to evaluate : 1.962 Fit side-chains REVERT: A 150 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: A 157 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: B 84 ASP cc_start: 0.7752 (t70) cc_final: 0.7509 (t0) REVERT: B 150 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: D 152 GLU cc_start: 0.7811 (tt0) cc_final: 0.7538 (tt0) REVERT: E 152 GLU cc_start: 0.8094 (tt0) cc_final: 0.7743 (tt0) REVERT: G 47 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7486 (mt) REVERT: H 125 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7574 (tm-30) REVERT: H 152 GLU cc_start: 0.7957 (tt0) cc_final: 0.7605 (tt0) REVERT: I 114 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: J 180 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8433 (ptpp) REVERT: K 102 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: L 128 ASN cc_start: 0.8666 (m-40) cc_final: 0.8448 (m-40) REVERT: L 154 TRP cc_start: 0.7110 (OUTLIER) cc_final: 0.6419 (m100) outliers start: 43 outliers final: 20 residues processed: 453 average time/residue: 2.0723 time to fit residues: 1007.9634 Evaluate side-chains 460 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 432 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 0.4980 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 30.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN C 42 ASN F 107 ASN G 42 ASN G 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16920 Z= 0.213 Angle : 0.548 4.346 22920 Z= 0.313 Chirality : 0.039 0.127 2508 Planarity : 0.004 0.030 2976 Dihedral : 3.917 14.808 2280 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.84 % Allowed : 17.48 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.19), residues: 2016 helix: 2.26 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.73 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 154 HIS 0.005 0.001 HIS A 146 PHE 0.010 0.002 PHE L 167 TYR 0.019 0.002 TYR I 123 ARG 0.005 0.000 ARG K 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 437 time to evaluate : 2.170 Fit side-chains REVERT: A 47 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 150 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: B 84 ASP cc_start: 0.7762 (t70) cc_final: 0.7523 (t0) REVERT: B 150 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: D 152 GLU cc_start: 0.7808 (tt0) cc_final: 0.7546 (tt0) REVERT: E 152 GLU cc_start: 0.8085 (tt0) cc_final: 0.7740 (tt0) REVERT: E 154 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.6335 (m100) REVERT: H 101 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6425 (tp30) REVERT: H 125 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7567 (tm-30) REVERT: H 152 GLU cc_start: 0.7960 (tt0) cc_final: 0.7598 (tt0) REVERT: I 114 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: J 180 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8438 (ptpp) REVERT: K 102 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6831 (mt-10) REVERT: K 157 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6734 (tp30) REVERT: L 128 ASN cc_start: 0.8688 (m-40) cc_final: 0.8447 (m-40) REVERT: L 154 TRP cc_start: 0.7130 (OUTLIER) cc_final: 0.6449 (m100) outliers start: 49 outliers final: 19 residues processed: 451 average time/residue: 2.0275 time to fit residues: 981.3619 Evaluate side-chains 459 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 430 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 157 GLU Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN G 42 ASN G 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16920 Z= 0.192 Angle : 0.521 4.385 22920 Z= 0.296 Chirality : 0.038 0.123 2508 Planarity : 0.004 0.030 2976 Dihedral : 3.813 14.163 2280 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.01 % Allowed : 18.23 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.19), residues: 2016 helix: 2.39 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.76 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 154 HIS 0.004 0.001 HIS J 43 PHE 0.008 0.001 PHE J 167 TYR 0.017 0.002 TYR I 123 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 424 time to evaluate : 2.160 Fit side-chains REVERT: A 150 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: B 84 ASP cc_start: 0.7763 (t70) cc_final: 0.7543 (t0) REVERT: B 150 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: D 152 GLU cc_start: 0.7780 (tt0) cc_final: 0.7515 (tt0) REVERT: E 152 GLU cc_start: 0.8055 (tt0) cc_final: 0.7718 (tt0) REVERT: E 154 TRP cc_start: 0.7335 (OUTLIER) cc_final: 0.6241 (m100) REVERT: H 101 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6416 (tp30) REVERT: H 152 GLU cc_start: 0.7940 (tt0) cc_final: 0.7540 (tt0) REVERT: I 114 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: I 116 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8384 (mm-30) REVERT: J 180 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8442 (ptpp) REVERT: K 102 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: L 154 TRP cc_start: 0.7012 (OUTLIER) cc_final: 0.6350 (m100) REVERT: L 157 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7111 (tm-30) outliers start: 52 outliers final: 21 residues processed: 440 average time/residue: 2.0563 time to fit residues: 971.2636 Evaluate side-chains 447 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 417 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 154 TRP Chi-restraints excluded: chain L residue 157 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 7.9990 chunk 22 optimal weight: 0.3980 chunk 112 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN F 107 ASN G 42 ASN G 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16920 Z= 0.227 Angle : 0.563 6.757 22920 Z= 0.321 Chirality : 0.039 0.130 2508 Planarity : 0.004 0.030 2976 Dihedral : 3.928 15.690 2280 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.07 % Allowed : 18.52 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.19), residues: 2016 helix: 2.25 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.71 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 154 HIS 0.005 0.001 HIS A 146 PHE 0.010 0.002 PHE J 167 TYR 0.020 0.002 TYR I 123 ARG 0.007 0.000 ARG L 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 435 time to evaluate : 2.198 Fit side-chains REVERT: A 47 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7387 (mt) REVERT: A 150 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: A 157 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: B 84 ASP cc_start: 0.7777 (t70) cc_final: 0.7544 (t0) REVERT: B 150 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: D 152 GLU cc_start: 0.7793 (tt0) cc_final: 0.7539 (tt0) REVERT: E 152 GLU cc_start: 0.8111 (tt0) cc_final: 0.7776 (tt0) REVERT: E 154 TRP cc_start: 0.7432 (OUTLIER) cc_final: 0.6357 (m100) REVERT: G 150 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: H 101 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6451 (tp30) REVERT: H 152 GLU cc_start: 0.7968 (tt0) cc_final: 0.7629 (tt0) REVERT: H 183 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7471 (mmtp) REVERT: I 80 GLU cc_start: 0.7219 (pm20) cc_final: 0.7015 (pm20) REVERT: I 114 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: I 116 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8349 (mm-30) REVERT: J 180 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8492 (pttp) REVERT: K 102 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6733 (mt-10) REVERT: L 154 TRP cc_start: 0.7165 (OUTLIER) cc_final: 0.6488 (m100) outliers start: 53 outliers final: 24 residues processed: 453 average time/residue: 2.1012 time to fit residues: 1022.2029 Evaluate side-chains 464 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 428 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 154 TRP Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 40.0000 chunk 59 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 125 optimal weight: 0.0370 chunk 133 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN G 42 ASN G 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16920 Z= 0.217 Angle : 0.552 6.247 22920 Z= 0.315 Chirality : 0.039 0.128 2508 Planarity : 0.004 0.033 2976 Dihedral : 3.898 15.358 2280 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.89 % Allowed : 18.92 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.19), residues: 2016 helix: 2.28 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.71 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 154 HIS 0.004 0.001 HIS J 43 PHE 0.009 0.002 PHE J 167 TYR 0.019 0.002 TYR I 123 ARG 0.007 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 426 time to evaluate : 1.775 Fit side-chains REVERT: A 47 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7348 (mt) REVERT: A 150 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: A 157 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: B 84 ASP cc_start: 0.7760 (t70) cc_final: 0.7524 (t0) REVERT: B 150 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: C 156 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: D 152 GLU cc_start: 0.7798 (tt0) cc_final: 0.7541 (tt0) REVERT: E 57 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: E 152 GLU cc_start: 0.8112 (tt0) cc_final: 0.7783 (tt0) REVERT: E 154 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.6335 (m100) REVERT: G 47 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7215 (mt) REVERT: G 150 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: H 101 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6442 (tp30) REVERT: H 152 GLU cc_start: 0.7966 (tt0) cc_final: 0.7622 (tt0) REVERT: H 183 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7506 (mmtp) REVERT: I 114 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: I 116 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8374 (mm-30) REVERT: J 180 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8494 (pttp) REVERT: K 102 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6708 (mt-10) REVERT: L 154 TRP cc_start: 0.7121 (OUTLIER) cc_final: 0.6378 (m100) outliers start: 50 outliers final: 27 residues processed: 443 average time/residue: 2.0441 time to fit residues: 971.2986 Evaluate side-chains 467 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 425 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 154 TRP Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 154 TRP Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 56 optimal weight: 40.0000 chunk 165 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN F 107 ASN G 42 ASN G 107 ASN K 151 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16920 Z= 0.228 Angle : 0.567 6.810 22920 Z= 0.323 Chirality : 0.040 0.131 2508 Planarity : 0.004 0.035 2976 Dihedral : 3.937 15.623 2280 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.95 % Allowed : 19.10 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.19), residues: 2016 helix: 2.22 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.69 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 154 HIS 0.005 0.001 HIS A 146 PHE 0.010 0.002 PHE J 167 TYR 0.020 0.002 TYR I 123 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 430 time to evaluate : 2.079 Fit side-chains REVERT: A 47 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7410 (mt) REVERT: A 150 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: A 157 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: B 84 ASP cc_start: 0.7778 (t70) cc_final: 0.7546 (t0) REVERT: B 150 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: C 156 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: D 152 GLU cc_start: 0.7800 (tt0) cc_final: 0.7548 (tt0) REVERT: E 57 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: E 152 GLU cc_start: 0.8100 (tt0) cc_final: 0.7772 (tt0) REVERT: E 154 TRP cc_start: 0.7441 (OUTLIER) cc_final: 0.6359 (m100) REVERT: G 47 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7233 (mt) REVERT: G 150 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: H 101 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6592 (tp30) REVERT: H 152 GLU cc_start: 0.7974 (tt0) cc_final: 0.7630 (tt0) REVERT: H 183 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7504 (mmtp) REVERT: I 114 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: I 116 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8378 (mm-30) REVERT: J 180 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8490 (pttp) REVERT: K 102 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: L 154 TRP cc_start: 0.7164 (OUTLIER) cc_final: 0.6438 (m100) outliers start: 51 outliers final: 28 residues processed: 448 average time/residue: 2.0363 time to fit residues: 978.1101 Evaluate side-chains 467 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 424 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 154 TRP Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 154 TRP Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 5.9990 chunk 118 optimal weight: 30.0000 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 0.0670 chunk 203 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 161 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN G 42 ASN G 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16920 Z= 0.160 Angle : 0.488 6.628 22920 Z= 0.272 Chirality : 0.037 0.120 2508 Planarity : 0.003 0.032 2976 Dihedral : 3.641 13.246 2280 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.91 % Allowed : 20.20 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.19), residues: 2016 helix: 2.65 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.84 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 154 HIS 0.004 0.001 HIS G 66 PHE 0.008 0.001 PHE H 167 TYR 0.013 0.001 TYR I 123 ARG 0.008 0.000 ARG L 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 2.104 Fit side-chains REVERT: B 150 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: D 152 GLU cc_start: 0.7677 (tt0) cc_final: 0.7429 (tt0) REVERT: E 57 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: E 152 GLU cc_start: 0.8002 (tt0) cc_final: 0.7646 (tt0) REVERT: G 150 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: H 152 GLU cc_start: 0.7767 (tt0) cc_final: 0.7395 (tt0) REVERT: I 114 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: I 116 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8455 (mm-30) REVERT: J 180 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8467 (ptpp) REVERT: L 154 TRP cc_start: 0.6871 (OUTLIER) cc_final: 0.6336 (m100) outliers start: 33 outliers final: 14 residues processed: 420 average time/residue: 1.9750 time to fit residues: 892.4164 Evaluate side-chains 401 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 381 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 154 TRP Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 154 TRP Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 114 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 166 optimal weight: 30.0000 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN B 128 ASN G 42 ASN G 107 ASN I 107 ASN J 42 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.168688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.156092 restraints weight = 11209.469| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 0.52 r_work: 0.3435 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16920 Z= 0.190 Angle : 0.519 6.826 22920 Z= 0.292 Chirality : 0.038 0.148 2508 Planarity : 0.004 0.055 2976 Dihedral : 3.732 14.158 2280 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.56 % Allowed : 21.01 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.19), residues: 2016 helix: 2.53 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.81 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 154 HIS 0.004 0.001 HIS A 146 PHE 0.009 0.001 PHE D 67 TYR 0.017 0.002 TYR I 123 ARG 0.007 0.000 ARG D 86 =============================================================================== Job complete usr+sys time: 12007.84 seconds wall clock time: 214 minutes 17.17 seconds (12857.17 seconds total)