Starting phenix.real_space_refine on Sun Mar 17 05:09:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stw_25437/03_2024/7stw_25437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stw_25437/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stw_25437/03_2024/7stw_25437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stw_25437/03_2024/7stw_25437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stw_25437/03_2024/7stw_25437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stw_25437/03_2024/7stw_25437.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.91, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 2.9 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: 1.38 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: 4.34 Time building geometry restraints manager: 6.65 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: 102.44 - 108.75: 684 108.75 - 115.05: 9664 115.05 - 121.36: 8901 121.36 - 127.66: 3552 127.66 - 133.97: 119 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 2.520 nonbonded pdb=" OE2 GLU F 68 " pdb=" O HOH K 301 " model vdw 2.027 2.440 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 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: 0.030 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: 1.220 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 43.620 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.440 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 1.963 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: 1.8810 time to fit residues: 1262.9115 Evaluate side-chains 480 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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: 20.0000 chunk 104 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 61 optimal weight: 40.0000 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 overall best weight: 13.5998 ------------------------------------------------------------------------------- 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: 0.8190 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16920 Z= 0.361 Angle : 0.755 5.864 22920 Z= 0.434 Chirality : 0.048 0.164 2508 Planarity : 0.006 0.050 2976 Dihedral : 4.370 19.148 2280 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.20 % Allowed : 13.54 % Favored : 84.26 % 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: 1.76 (0.19), residues: 2016 helix: 1.57 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.32 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP K 154 HIS 0.010 0.003 HIS H 146 PHE 0.017 0.003 PHE A 88 TYR 0.027 0.004 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 543 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 505 time to evaluate : 1.966 Fit side-chains revert: symmetry clash REVERT: B 84 ASP cc_start: 0.7903 (t70) cc_final: 0.7577 (t0) REVERT: B 128 ASN cc_start: 0.9027 (m-40) cc_final: 0.8688 (m-40) REVERT: B 150 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: F 52 ILE cc_start: 0.8812 (pt) cc_final: 0.8601 (pt) REVERT: F 83 ARG cc_start: 0.8602 (ttt90) cc_final: 0.8386 (ttt-90) REVERT: H 152 GLU cc_start: 0.7981 (tt0) cc_final: 0.7673 (tt0) REVERT: I 162 LYS cc_start: 0.7778 (ttpp) cc_final: 0.7516 (tttp) REVERT: J 106 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6838 (tt0) REVERT: J 133 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7692 (mtmt) REVERT: J 150 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: J 180 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8591 (pttp) REVERT: K 162 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7123 (ttmt) REVERT: L 14 ILE cc_start: 0.7288 (pt) cc_final: 0.7044 (pt) REVERT: L 25 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8631 (mtpt) REVERT: L 154 TRP cc_start: 0.7543 (OUTLIER) cc_final: 0.6762 (m100) outliers start: 38 outliers final: 11 residues processed: 512 average time/residue: 1.8766 time to fit residues: 1031.0121 Evaluate side-chains 512 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 494 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 179 SER Chi-restraints excluded: chain G residue 16 VAL 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 106 GLU 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 K residue 162 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: 1.9990 chunk 154 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 16920 Z= 0.233 Angle : 0.588 4.453 22920 Z= 0.337 Chirality : 0.041 0.134 2508 Planarity : 0.004 0.031 2976 Dihedral : 4.054 16.059 2280 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.84 % Allowed : 15.80 % Favored : 81.37 % 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: 2.37 (0.19), residues: 2016 helix: 2.03 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.54 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 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 0.001 ARG L 95 *********************** 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 510 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 461 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 154 TRP cc_start: 0.7606 (OUTLIER) cc_final: 0.7335 (m100) REVERT: B 84 ASP cc_start: 0.7784 (t70) cc_final: 0.7528 (t0) REVERT: B 150 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: C 114 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: D 152 GLU cc_start: 0.7818 (tt0) cc_final: 0.7577 (tt0) REVERT: D 157 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6546 (tm-30) REVERT: E 152 GLU cc_start: 0.8132 (tt0) cc_final: 0.7793 (tt0) REVERT: E 154 TRP cc_start: 0.7490 (OUTLIER) cc_final: 0.6519 (m100) REVERT: F 52 ILE cc_start: 0.8638 (pt) cc_final: 0.8408 (pt) REVERT: H 125 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7543 (tm-30) REVERT: H 152 GLU cc_start: 0.7944 (tt0) cc_final: 0.7624 (tt0) REVERT: I 62 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8120 (mm-30) REVERT: I 114 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: K 157 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: L 128 ASN cc_start: 0.8727 (m-40) cc_final: 0.8508 (m-40) REVERT: L 150 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: L 152 GLU cc_start: 0.7849 (tt0) cc_final: 0.7633 (tt0) REVERT: L 154 TRP cc_start: 0.7290 (OUTLIER) cc_final: 0.6526 (m100) outliers start: 49 outliers final: 17 residues processed: 471 average time/residue: 1.9356 time to fit residues: 976.9485 Evaluate side-chains 460 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 435 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 LYS 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 114 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 TRP 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 F residue 54 GLU 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 K residue 157 GLU Chi-restraints excluded: chain L 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: 10.0000 chunk 139 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 176 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN F 42 ASN K 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16920 Z= 0.228 Angle : 0.570 4.354 22920 Z= 0.327 Chirality : 0.040 0.133 2508 Planarity : 0.004 0.030 2976 Dihedral : 3.987 15.965 2280 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.95 % Allowed : 16.44 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.19), residues: 2016 helix: 2.13 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.63 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 154 HIS 0.005 0.001 HIS A 146 PHE 0.010 0.002 PHE K 167 TYR 0.019 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 488 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 437 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: A 150 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: A 157 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7070 (tt0) REVERT: B 84 ASP cc_start: 0.7778 (t70) cc_final: 0.7505 (t0) REVERT: B 150 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: E 152 GLU cc_start: 0.8074 (tt0) cc_final: 0.7725 (tt0) REVERT: E 154 TRP cc_start: 0.7470 (OUTLIER) cc_final: 0.6433 (m100) REVERT: H 101 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: H 125 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7547 (tm-30) REVERT: H 152 GLU cc_start: 0.7936 (tt0) cc_final: 0.7605 (tt0) REVERT: I 86 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7842 (mtm-85) REVERT: I 114 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: J 180 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8526 (pttp) REVERT: K 102 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: L 128 ASN cc_start: 0.8768 (m-40) cc_final: 0.8500 (m-40) REVERT: L 150 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: L 154 TRP cc_start: 0.7249 (OUTLIER) cc_final: 0.6556 (m100) outliers start: 51 outliers final: 19 residues processed: 451 average time/residue: 1.8991 time to fit residues: 919.4637 Evaluate side-chains 461 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 431 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 117 ARG 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 162 LYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 154 TRP 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 86 ARG 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 102 GLU Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain L residue 150 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: 7.9990 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 168 optimal weight: 0.0270 chunk 136 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 overall best weight: 5.8046 ------------------------------------------------------------------------------- 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 42 ASN G 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4106 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= 0.214 Angle : 0.546 4.335 22920 Z= 0.312 Chirality : 0.039 0.129 2508 Planarity : 0.004 0.031 2976 Dihedral : 3.903 15.517 2280 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.01 % Allowed : 17.42 % Favored : 79.57 % 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 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 154 HIS 0.005 0.001 HIS A 146 PHE 0.010 0.002 PHE A 167 TYR 0.018 0.002 TYR I 123 ARG 0.006 0.000 ARG D 86 *********************** 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 485 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 433 time to evaluate : 2.057 Fit side-chains REVERT: A 47 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7520 (mt) REVERT: A 150 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: B 84 ASP cc_start: 0.7754 (t70) cc_final: 0.7503 (t0) REVERT: B 150 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: D 152 GLU cc_start: 0.7804 (tt0) cc_final: 0.7578 (tt0) REVERT: E 57 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: E 152 GLU cc_start: 0.8107 (tt0) cc_final: 0.7760 (tt0) REVERT: E 154 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.6381 (m100) REVERT: H 101 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6381 (tp30) REVERT: H 152 GLU cc_start: 0.7928 (tt0) cc_final: 0.7644 (tt0) REVERT: I 114 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: I 116 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8420 (mm-30) REVERT: J 180 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8526 (pttp) REVERT: K 102 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6675 (mt-10) REVERT: K 157 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: L 14 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.6173 (pp) REVERT: L 106 GLU cc_start: 0.6474 (mp0) cc_final: 0.6274 (mp0) REVERT: L 128 ASN cc_start: 0.8691 (m-40) cc_final: 0.8432 (m-40) REVERT: L 150 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: L 154 TRP cc_start: 0.7213 (OUTLIER) cc_final: 0.6542 (m100) outliers start: 52 outliers final: 23 residues processed: 450 average time/residue: 1.9096 time to fit residues: 921.9888 Evaluate side-chains 465 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 429 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 53 LYS 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 54 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 150 GLU 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 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 K residue 174 GLU Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 150 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: 50.0000 chunk 177 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 65 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 overall best weight: 4.5984 ------------------------------------------------------------------------------- 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 42 ASN G 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16920 Z= 0.195 Angle : 0.520 4.937 22920 Z= 0.296 Chirality : 0.038 0.123 2508 Planarity : 0.004 0.028 2976 Dihedral : 3.793 15.981 2280 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.78 % Allowed : 18.29 % Favored : 78.94 % 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: 2.40 (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 A 154 HIS 0.004 0.001 HIS J 43 PHE 0.009 0.002 PHE A 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 475 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 427 time to evaluate : 1.938 Fit side-chains REVERT: A 47 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7320 (mt) REVERT: A 150 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: A 157 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6713 (tt0) REVERT: B 84 ASP cc_start: 0.7757 (t70) cc_final: 0.7540 (t0) REVERT: B 150 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: D 152 GLU cc_start: 0.7800 (tt0) cc_final: 0.7553 (tt0) REVERT: E 152 GLU cc_start: 0.8084 (tt0) cc_final: 0.7737 (tt0) REVERT: E 154 TRP cc_start: 0.7354 (OUTLIER) cc_final: 0.6284 (m100) REVERT: G 150 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: H 101 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6399 (tp30) REVERT: H 125 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7494 (tm-30) REVERT: H 152 GLU cc_start: 0.7916 (tt0) cc_final: 0.7590 (tt0) REVERT: I 86 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7908 (mtm-85) REVERT: I 114 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: I 116 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8429 (mm-30) REVERT: J 180 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8436 (ptpp) REVERT: K 102 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: L 128 ASN cc_start: 0.8611 (m-40) cc_final: 0.8383 (m-40) REVERT: L 150 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: L 154 TRP cc_start: 0.7116 (OUTLIER) cc_final: 0.6423 (m100) outliers start: 48 outliers final: 20 residues processed: 447 average time/residue: 1.9032 time to fit residues: 912.3157 Evaluate side-chains 455 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 422 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 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 B residue 179 SER 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 120 VAL 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 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 I residue 86 ARG 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 174 GLU Chi-restraints excluded: chain L residue 150 GLU Chi-restraints excluded: chain L residue 154 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 90 optimal weight: 7.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- 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: 0.8088 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16920 Z= 0.222 Angle : 0.551 4.327 22920 Z= 0.314 Chirality : 0.039 0.140 2508 Planarity : 0.004 0.030 2976 Dihedral : 3.889 15.830 2280 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.01 % Allowed : 18.52 % Favored : 78.47 % 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 : 0.72 (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 0.011 0.002 PHE D 167 TYR 0.019 0.002 TYR I 123 ARG 0.006 0.000 ARG D 86 *********************** 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 491 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 439 time to evaluate : 1.813 Fit side-chains REVERT: A 150 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: A 157 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: B 84 ASP cc_start: 0.7757 (t70) cc_final: 0.7513 (t0) REVERT: B 150 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: D 152 GLU cc_start: 0.7811 (tt0) cc_final: 0.7578 (tt0) REVERT: E 152 GLU cc_start: 0.8076 (tt0) cc_final: 0.7741 (tt0) REVERT: E 154 TRP cc_start: 0.7425 (OUTLIER) cc_final: 0.6358 (m100) REVERT: G 47 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7223 (mt) REVERT: G 150 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: H 101 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6522 (tp30) REVERT: H 152 GLU cc_start: 0.7932 (tt0) cc_final: 0.7608 (tt0) REVERT: H 183 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7470 (mmtp) REVERT: I 86 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7920 (mtm-85) REVERT: I 114 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: I 116 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8375 (mm-30) REVERT: J 180 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8526 (pttp) REVERT: K 102 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6756 (mt-10) REVERT: K 157 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: L 14 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.6200 (pp) REVERT: L 128 ASN cc_start: 0.8695 (m-40) cc_final: 0.8429 (m-40) REVERT: L 150 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: L 154 TRP cc_start: 0.7217 (OUTLIER) cc_final: 0.6505 (m100) outliers start: 52 outliers final: 28 residues processed: 457 average time/residue: 1.8818 time to fit residues: 923.9579 Evaluate side-chains 470 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 426 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 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 B residue 179 SER 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 120 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 154 TRP Chi-restraints excluded: chain E residue 179 SER 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 150 GLU 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 86 ARG 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 106 GLU Chi-restraints excluded: chain J residue 114 GLU 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 K residue 157 GLU Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 150 GLU 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: 7.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.8084 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16920 Z= 0.220 Angle : 0.550 4.357 22920 Z= 0.313 Chirality : 0.039 0.128 2508 Planarity : 0.004 0.036 2976 Dihedral : 3.879 15.278 2280 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.30 % Allowed : 18.34 % Favored : 78.36 % 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 : 0.72 (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 0.018 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 486 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 429 time to evaluate : 1.989 Fit side-chains REVERT: A 150 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: A 157 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: B 84 ASP cc_start: 0.7744 (t70) cc_final: 0.7527 (t0) REVERT: B 150 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: C 114 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: D 152 GLU cc_start: 0.7850 (tt0) cc_final: 0.7635 (tt0) REVERT: E 152 GLU cc_start: 0.8052 (tt0) cc_final: 0.7745 (tt0) REVERT: E 154 TRP cc_start: 0.7419 (OUTLIER) cc_final: 0.6368 (m100) REVERT: G 47 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7221 (mt) REVERT: G 150 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: H 101 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6520 (tp30) REVERT: H 152 GLU cc_start: 0.7905 (tt0) cc_final: 0.7646 (tt0) REVERT: H 183 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7464 (mmtp) REVERT: I 54 GLU cc_start: 0.7291 (pp20) cc_final: 0.7024 (pp20) REVERT: I 86 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7934 (mtm-85) REVERT: I 114 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: I 116 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8403 (mm-30) REVERT: J 180 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8523 (pttp) REVERT: K 102 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: K 157 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: L 14 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6204 (pp) REVERT: L 128 ASN cc_start: 0.8730 (m-40) cc_final: 0.8460 (m-40) REVERT: L 150 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: L 154 TRP cc_start: 0.7201 (OUTLIER) cc_final: 0.6492 (m100) outliers start: 57 outliers final: 31 residues processed: 446 average time/residue: 1.8798 time to fit residues: 900.6493 Evaluate side-chains 475 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 427 time to evaluate : 1.911 ------------------------------------------------------------------------------- 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 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 B residue 179 SER Chi-restraints excluded: chain C residue 114 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 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 E residue 179 SER 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 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 86 ARG 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 106 GLU Chi-restraints excluded: chain J residue 114 GLU 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 K residue 157 GLU Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 150 GLU Chi-restraints excluded: chain L residue 154 TRP Chi-restraints excluded: chain L residue 162 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 110 optimal weight: 0.0030 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 56 optimal weight: 40.0000 chunk 165 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 overall best weight: 4.5998 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16920 Z= 0.199 Angle : 0.525 5.842 22920 Z= 0.298 Chirality : 0.038 0.124 2508 Planarity : 0.004 0.031 2976 Dihedral : 3.778 16.955 2280 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.89 % Allowed : 18.75 % Favored : 78.36 % 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: 2.91 (0.19), residues: 2016 helix: 2.42 (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 A 154 HIS 0.005 0.001 HIS J 43 PHE 0.009 0.002 PHE J 167 TYR 0.017 0.002 TYR I 123 ARG 0.007 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 473 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 423 time to evaluate : 1.921 Fit side-chains REVERT: A 47 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7135 (mt) REVERT: A 157 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6716 (tt0) REVERT: B 150 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: D 152 GLU cc_start: 0.7784 (tt0) cc_final: 0.7552 (tt0) REVERT: E 152 GLU cc_start: 0.8020 (tt0) cc_final: 0.7703 (tt0) REVERT: E 154 TRP cc_start: 0.7332 (OUTLIER) cc_final: 0.6202 (m100) REVERT: H 152 GLU cc_start: 0.7909 (tt0) cc_final: 0.7610 (tt0) REVERT: I 86 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7914 (mtm-85) REVERT: I 114 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: J 180 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8431 (ptpp) REVERT: K 102 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: K 157 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6814 (tt0) REVERT: L 14 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.6115 (pp) REVERT: L 57 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: L 150 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: L 154 TRP cc_start: 0.7114 (OUTLIER) cc_final: 0.6435 (m100) outliers start: 50 outliers final: 27 residues processed: 443 average time/residue: 1.9316 time to fit residues: 917.1751 Evaluate side-chains 459 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 419 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 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 122 VAL 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 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 E residue 179 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 154 TRP Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 86 ARG 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 K residue 154 TRP Chi-restraints excluded: chain K residue 157 GLU Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 150 GLU 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: 9.9990 chunk 118 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 chunk 203 optimal weight: 0.5980 chunk 187 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 16 optimal weight: 0.1980 chunk 125 optimal weight: 0.0570 chunk 99 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 overall best weight: 1.5100 ------------------------------------------------------------------------------- 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: 0.7852 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16920 Z= 0.152 Angle : 0.464 5.463 22920 Z= 0.257 Chirality : 0.036 0.118 2508 Planarity : 0.003 0.028 2976 Dihedral : 3.514 15.468 2280 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.68 % Allowed : 20.20 % Favored : 78.12 % 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: 3.40 (0.20), residues: 2016 helix: 2.85 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : 0.79 (0.30), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 154 HIS 0.003 0.001 HIS E 146 PHE 0.007 0.001 PHE I 88 TYR 0.017 0.001 TYR H 129 ARG 0.006 0.000 ARG D 86 ********************** 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 423 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 394 time to evaluate : 2.081 Fit side-chains REVERT: B 150 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: C 80 GLU cc_start: 0.7500 (pm20) cc_final: 0.7268 (pm20) REVERT: D 152 GLU cc_start: 0.7695 (tt0) cc_final: 0.7356 (tt0) REVERT: E 152 GLU cc_start: 0.7844 (tt0) cc_final: 0.7523 (tt0) REVERT: H 152 GLU cc_start: 0.7614 (tt0) cc_final: 0.7277 (tt0) REVERT: I 86 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7838 (mtm-85) REVERT: J 180 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8463 (ptpp) REVERT: L 14 ILE cc_start: 0.6111 (OUTLIER) cc_final: 0.5751 (pp) REVERT: L 154 TRP cc_start: 0.6832 (OUTLIER) cc_final: 0.6405 (m100) outliers start: 29 outliers final: 12 residues processed: 411 average time/residue: 1.9033 time to fit residues: 839.4781 Evaluate side-chains 386 residues out of total 1728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 369 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL 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 122 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 154 TRP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 154 TRP Chi-restraints excluded: chain H residue 154 TRP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 180 LYS Chi-restraints excluded: chain K residue 174 GLU Chi-restraints excluded: chain L residue 14 ILE 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: 5.9990 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 162 optimal weight: 0.0170 chunk 67 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 overall best weight: 3.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN E 128 ASN G 107 ASN J 42 ASN J 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.171110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.158550 restraints weight = 11396.177| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 0.53 r_work: 0.3486 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16920 Z= 0.175 Angle : 0.491 5.446 22920 Z= 0.274 Chirality : 0.036 0.122 2508 Planarity : 0.003 0.029 2976 Dihedral : 3.550 14.969 2280 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.33 % Allowed : 21.64 % Favored : 77.03 % 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: 3.24 (0.19), residues: 2016 helix: 2.68 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : 0.85 (0.30), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 154 HIS 0.004 0.001 HIS F 146 PHE 0.008 0.001 PHE D 67 TYR 0.014 0.001 TYR K 123 ARG 0.008 0.000 ARG K 95 =============================================================================== Job complete usr+sys time: 11630.12 seconds wall clock time: 202 minutes 32.22 seconds (12152.22 seconds total)