Starting phenix.real_space_refine on Sat Mar 16 08:41:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k36_36845/03_2024/8k36_36845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k36_36845/03_2024/8k36_36845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k36_36845/03_2024/8k36_36845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k36_36845/03_2024/8k36_36845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k36_36845/03_2024/8k36_36845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k36_36845/03_2024/8k36_36845.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 8892 2.51 5 N 2400 2.21 5 O 2844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ASP 104": "OD1" <-> "OD2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "F ASP 35": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G ASP 44": "OD1" <-> "OD2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G ASP 104": "OD1" <-> "OD2" Residue "H ASP 25": "OD1" <-> "OD2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H ASP 104": "OD1" <-> "OD2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H ASP 154": "OD1" <-> "OD2" Residue "I ASP 35": "OD1" <-> "OD2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I ASP 56": "OD1" <-> "OD2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I ASP 104": "OD1" <-> "OD2" Residue "J ASP 25": "OD1" <-> "OD2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J ASP 104": "OD1" <-> "OD2" Residue "K ASP 25": "OD1" <-> "OD2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K ASP 104": "OD1" <-> "OD2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K ASP 154": "OD1" <-> "OD2" Residue "L ASP 35": "OD1" <-> "OD2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L ASP 104": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14172 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "B" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "C" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "D" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "E" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "F" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "H" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "I" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "J" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "K" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "L" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1181 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Time building chain proxies: 7.43, per 1000 atoms: 0.52 Number of scatterers: 14172 At special positions: 0 Unit cell: (110.16, 110.16, 108.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2844 8.00 N 2400 7.00 C 8892 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: 4.86 Conformation dependent library (CDL) restraints added in 2.6 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 32 sheets defined 9.5% alpha, 44.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.501A pdb=" N GLN A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.646A pdb=" N ARG A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.649A pdb=" N ARG D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'G' and resid 90 through 102 removed outlier: 3.500A pdb=" N GLN G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.645A pdb=" N ARG G 155 " --> pdb=" O ALA G 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'I' and resid 90 through 102 Processing helix chain 'J' and resid 90 through 102 Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.648A pdb=" N ARG J 155 " --> pdb=" O ALA J 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 102 Processing helix chain 'L' and resid 90 through 102 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.534A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS A 142 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 127 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 140 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 129 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 138 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER A 81 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 45 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR A 83 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.534A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 removed outlier: 5.269A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 17 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 51 removed outlier: 5.161A pdb=" N VAL B 124 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR B 144 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 138 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER B 81 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU B 45 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR B 83 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 76 removed outlier: 5.817A pdb=" N GLU B 53 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 75 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 51 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER C 125 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N SER B 54 " --> pdb=" O TRP C 123 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N TRP C 123 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 14.551A pdb=" N ASP B 56 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 18.179A pdb=" N ARG C 121 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA C 107 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 17 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 76 removed outlier: 5.817A pdb=" N GLU B 53 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 75 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 51 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER C 125 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N SER B 54 " --> pdb=" O TRP C 123 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N TRP C 123 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 14.551A pdb=" N ASP B 56 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 18.179A pdb=" N ARG C 121 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS C 142 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 127 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 140 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS C 129 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR C 138 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER C 81 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU C 45 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 83 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 51 removed outlier: 5.345A pdb=" N ALA D 107 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU D 17 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.565A pdb=" N LYS D 142 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE D 127 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR D 140 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS D 129 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR D 138 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER D 81 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU D 45 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR D 83 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 54 through 56 Processing sheet with id=AB2, first strand: chain 'D' and resid 50 through 51 removed outlier: 5.270A pdb=" N ALA E 107 " --> pdb=" O TYR E 20 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU E 17 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 51 removed outlier: 5.160A pdb=" N VAL E 124 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR E 144 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 138 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER E 81 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU E 45 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR E 83 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AB5, first strand: chain 'E' and resid 70 through 76 removed outlier: 5.812A pdb=" N GLU E 53 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS E 75 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR E 51 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER F 125 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N SER E 54 " --> pdb=" O TRP F 123 " (cutoff:3.500A) removed outlier: 12.214A pdb=" N TRP F 123 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 14.548A pdb=" N ASP E 56 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 18.172A pdb=" N ARG F 121 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA F 107 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU F 17 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 70 through 76 removed outlier: 5.812A pdb=" N GLU E 53 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS E 75 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR E 51 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER F 125 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N SER E 54 " --> pdb=" O TRP F 123 " (cutoff:3.500A) removed outlier: 12.214A pdb=" N TRP F 123 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 14.548A pdb=" N ASP E 56 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 18.172A pdb=" N ARG F 121 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS F 142 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE F 127 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR F 140 " --> pdb=" O ILE F 127 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS F 129 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR F 138 " --> pdb=" O LYS F 129 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER F 81 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU F 45 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR F 83 " --> pdb=" O LYS F 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 54 through 56 Processing sheet with id=AB8, first strand: chain 'G' and resid 36 through 39 removed outlier: 4.533A pdb=" N LEU G 17 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA G 107 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS G 142 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE G 127 " --> pdb=" O THR G 140 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR G 140 " --> pdb=" O ILE G 127 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS G 129 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR G 138 " --> pdb=" O LYS G 129 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER G 81 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU G 45 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR G 83 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 36 through 39 removed outlier: 4.533A pdb=" N LEU G 17 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA G 107 " --> pdb=" O TYR G 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 50 through 51 removed outlier: 5.270A pdb=" N ALA H 107 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU H 17 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 50 through 51 removed outlier: 5.162A pdb=" N VAL H 124 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR H 144 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR H 138 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N SER H 81 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU H 45 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR H 83 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 54 through 56 Processing sheet with id=AC4, first strand: chain 'H' and resid 70 through 76 removed outlier: 5.816A pdb=" N GLU H 53 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS H 75 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR H 51 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER I 125 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SER H 54 " --> pdb=" O TRP I 123 " (cutoff:3.500A) removed outlier: 12.212A pdb=" N TRP I 123 " --> pdb=" O SER H 54 " (cutoff:3.500A) removed outlier: 14.552A pdb=" N ASP H 56 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 18.180A pdb=" N ARG I 121 " --> pdb=" O ASP H 56 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA I 107 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU I 17 " --> pdb=" O LEU I 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 70 through 76 removed outlier: 5.816A pdb=" N GLU H 53 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS H 75 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR H 51 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER I 125 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SER H 54 " --> pdb=" O TRP I 123 " (cutoff:3.500A) removed outlier: 12.212A pdb=" N TRP I 123 " --> pdb=" O SER H 54 " (cutoff:3.500A) removed outlier: 14.552A pdb=" N ASP H 56 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 18.180A pdb=" N ARG I 121 " --> pdb=" O ASP H 56 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS I 142 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE I 127 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR I 140 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS I 129 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR I 138 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER I 81 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU I 45 " --> pdb=" O SER I 81 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR I 83 " --> pdb=" O LYS I 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 50 through 51 removed outlier: 5.345A pdb=" N ALA J 107 " --> pdb=" O TYR J 20 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU J 17 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 50 through 51 removed outlier: 6.565A pdb=" N LYS J 142 " --> pdb=" O SER J 125 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE J 127 " --> pdb=" O THR J 140 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR J 140 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS J 129 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR J 138 " --> pdb=" O LYS J 129 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER J 81 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU J 45 " --> pdb=" O SER J 81 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR J 83 " --> pdb=" O LYS J 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 54 through 56 Processing sheet with id=AC9, first strand: chain 'J' and resid 50 through 51 removed outlier: 5.270A pdb=" N ALA K 107 " --> pdb=" O TYR K 20 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU K 17 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 50 through 51 removed outlier: 5.160A pdb=" N VAL K 124 " --> pdb=" O THR K 144 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR K 144 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR K 138 " --> pdb=" O ALA K 130 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER K 81 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU K 45 " --> pdb=" O SER K 81 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR K 83 " --> pdb=" O LYS K 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 54 through 56 Processing sheet with id=AD3, first strand: chain 'K' and resid 70 through 76 removed outlier: 5.811A pdb=" N GLU K 53 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS K 75 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR K 51 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER L 125 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SER K 54 " --> pdb=" O TRP L 123 " (cutoff:3.500A) removed outlier: 12.213A pdb=" N TRP L 123 " --> pdb=" O SER K 54 " (cutoff:3.500A) removed outlier: 14.546A pdb=" N ASP K 56 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 18.171A pdb=" N ARG L 121 " --> pdb=" O ASP K 56 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA L 107 " --> pdb=" O TYR L 20 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU L 17 " --> pdb=" O LEU L 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 70 through 76 removed outlier: 5.811A pdb=" N GLU K 53 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS K 75 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR K 51 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER L 125 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SER K 54 " --> pdb=" O TRP L 123 " (cutoff:3.500A) removed outlier: 12.213A pdb=" N TRP L 123 " --> pdb=" O SER K 54 " (cutoff:3.500A) removed outlier: 14.546A pdb=" N ASP K 56 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 18.171A pdb=" N ARG L 121 " --> pdb=" O ASP K 56 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS L 142 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE L 127 " --> pdb=" O THR L 140 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR L 140 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS L 129 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR L 138 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER L 81 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU L 45 " --> pdb=" O SER L 81 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR L 83 " --> pdb=" O LYS L 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 54 through 56 526 hydrogen bonds defined for protein. 1416 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: 3.72 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2515 1.31 - 1.44: 3915 1.44 - 1.56: 8018 1.56 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 14520 Sorted by residual: bond pdb=" CA GLY I 103 " pdb=" C GLY I 103 " ideal model delta sigma weight residual 1.519 1.461 0.057 9.70e-03 1.06e+04 3.50e+01 bond pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 1.519 1.462 0.057 9.70e-03 1.06e+04 3.45e+01 bond pdb=" CA GLU C 102 " pdb=" C GLU C 102 " ideal model delta sigma weight residual 1.525 1.454 0.071 1.29e-02 6.01e+03 3.01e+01 bond pdb=" CA GLU I 102 " pdb=" C GLU I 102 " ideal model delta sigma weight residual 1.525 1.454 0.071 1.29e-02 6.01e+03 3.00e+01 bond pdb=" CA GLN G 91 " pdb=" C GLN G 91 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.35e-02 5.49e+03 1.86e+01 ... (remaining 14515 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.19: 581 107.19 - 113.90: 8094 113.90 - 120.61: 5328 120.61 - 127.32: 5535 127.32 - 134.03: 262 Bond angle restraints: 19800 Sorted by residual: angle pdb=" N ASP F 61 " pdb=" CA ASP F 61 " pdb=" C ASP F 61 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" N ASP L 61 " pdb=" CA ASP L 61 " pdb=" C ASP L 61 " ideal model delta sigma weight residual 111.28 116.78 -5.50 1.09e+00 8.42e-01 2.55e+01 angle pdb=" N ASP I 61 " pdb=" CA ASP I 61 " pdb=" C ASP I 61 " ideal model delta sigma weight residual 111.28 116.75 -5.47 1.09e+00 8.42e-01 2.52e+01 angle pdb=" N ASP C 61 " pdb=" CA ASP C 61 " pdb=" C ASP C 61 " ideal model delta sigma weight residual 111.28 116.74 -5.46 1.09e+00 8.42e-01 2.51e+01 angle pdb=" N ASP C 62 " pdb=" CA ASP C 62 " pdb=" C ASP C 62 " ideal model delta sigma weight residual 110.24 117.04 -6.80 1.41e+00 5.03e-01 2.32e+01 ... (remaining 19795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7886 17.75 - 35.51: 532 35.51 - 53.26: 74 53.26 - 71.01: 14 71.01 - 88.77: 14 Dihedral angle restraints: 8520 sinusoidal: 3288 harmonic: 5232 Sorted by residual: dihedral pdb=" C GLU I 102 " pdb=" N GLU I 102 " pdb=" CA GLU I 102 " pdb=" CB GLU I 102 " ideal model delta harmonic sigma weight residual -122.60 -112.62 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C GLU C 102 " pdb=" N GLU C 102 " pdb=" CA GLU C 102 " pdb=" CB GLU C 102 " ideal model delta harmonic sigma weight residual -122.60 -112.62 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C ARG E 139 " pdb=" N ARG E 139 " pdb=" CA ARG E 139 " pdb=" CB ARG E 139 " ideal model delta harmonic sigma weight residual -122.60 -113.61 -8.99 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1900 0.087 - 0.175: 228 0.175 - 0.262: 14 0.262 - 0.349: 0 0.349 - 0.436: 6 Chirality restraints: 2148 Sorted by residual: chirality pdb=" CA ASP F 62 " pdb=" N ASP F 62 " pdb=" C ASP F 62 " pdb=" CB ASP F 62 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ASP I 62 " pdb=" N ASP I 62 " pdb=" C ASP I 62 " pdb=" CB ASP I 62 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ASP C 62 " pdb=" N ASP C 62 " pdb=" C ASP C 62 " pdb=" CB ASP C 62 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 2145 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 90 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C GLU G 90 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU G 90 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN G 91 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 90 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C GLU A 90 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU A 90 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN A 91 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 31 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C LEU A 31 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 31 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 32 " 0.012 2.00e-02 2.50e+03 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3173 2.78 - 3.31: 11954 3.31 - 3.84: 20948 3.84 - 4.37: 24600 4.37 - 4.90: 46736 Nonbonded interactions: 107411 Sorted by model distance: nonbonded pdb=" OH TYR F 108 " pdb=" OD1 ASN F 145 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR L 108 " pdb=" OD1 ASN L 145 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR I 108 " pdb=" OD1 ASN I 145 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR C 108 " pdb=" OD1 ASN C 145 " model vdw 2.259 2.440 nonbonded pdb=" OD1 ASP D 44 " pdb=" N LEU D 45 " model vdw 2.266 2.520 ... (remaining 107406 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.010 Extract box with map and model: 2.430 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.800 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.008 0.071 14520 Z= 0.532 Angle : 0.812 9.889 19800 Z= 0.463 Chirality : 0.057 0.436 2148 Planarity : 0.004 0.030 2580 Dihedral : 12.359 88.766 5184 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.80 % Allowed : 0.80 % Favored : 98.40 % 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: -0.90 (0.17), residues: 1824 helix: 1.22 (0.47), residues: 144 sheet: -0.16 (0.17), residues: 864 loop : -1.37 (0.15), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 18 PHE 0.017 0.002 PHE B 120 TYR 0.012 0.002 TYR K 20 ARG 0.004 0.001 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 370 time to evaluate : 1.438 Fit side-chains REVERT: A 61 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8414 (m-30) REVERT: A 134 LYS cc_start: 0.9186 (mtpt) cc_final: 0.8831 (mtmt) REVERT: B 27 TYR cc_start: 0.8889 (m-10) cc_final: 0.8634 (m-80) REVERT: C 11 LYS cc_start: 0.9427 (mttp) cc_final: 0.9182 (mttm) REVERT: C 41 LYS cc_start: 0.9401 (mttm) cc_final: 0.9165 (mttt) REVERT: C 43 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8300 (mtpp) REVERT: C 61 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: C 87 MET cc_start: 0.9238 (mtp) cc_final: 0.8941 (mtp) REVERT: C 114 ASN cc_start: 0.8767 (t0) cc_final: 0.8554 (t0) REVERT: C 134 LYS cc_start: 0.9273 (mtmt) cc_final: 0.9069 (mtmt) REVERT: D 44 ASP cc_start: 0.7826 (t0) cc_final: 0.7590 (t70) REVERT: D 118 ASP cc_start: 0.7839 (t0) cc_final: 0.7493 (t0) REVERT: E 11 LYS cc_start: 0.9337 (mttp) cc_final: 0.9106 (mttm) REVERT: F 61 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: F 87 MET cc_start: 0.9037 (mtp) cc_final: 0.8756 (mtp) REVERT: G 27 TYR cc_start: 0.8997 (m-10) cc_final: 0.8748 (m-10) REVERT: G 53 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7447 (mp0) REVERT: G 101 ASN cc_start: 0.8676 (m-40) cc_final: 0.8451 (m-40) REVERT: I 43 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8341 (mptt) REVERT: K 43 LYS cc_start: 0.9091 (mtpp) cc_final: 0.7670 (mmtt) REVERT: L 43 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8104 (mptt) REVERT: L 121 ARG cc_start: 0.8551 (mtp-110) cc_final: 0.8162 (ttm-80) outliers start: 12 outliers final: 0 residues processed: 372 average time/residue: 0.3110 time to fit residues: 157.5312 Evaluate side-chains 218 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain F residue 61 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN B 101 ASN F 94 GLN G 101 ASN J 101 ASN K 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14520 Z= 0.276 Angle : 0.554 5.102 19800 Z= 0.293 Chirality : 0.046 0.160 2148 Planarity : 0.004 0.028 2580 Dihedral : 5.108 57.297 1986 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.33 % Allowed : 9.40 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 1824 helix: 1.36 (0.43), residues: 144 sheet: -0.47 (0.15), residues: 948 loop : -1.02 (0.15), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 36 PHE 0.017 0.002 PHE B 120 TYR 0.016 0.002 TYR C 108 ARG 0.005 0.001 ARG I 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 243 time to evaluate : 1.639 Fit side-chains REVERT: A 134 LYS cc_start: 0.9288 (mtpt) cc_final: 0.8999 (mtmt) REVERT: B 61 ASP cc_start: 0.8111 (m-30) cc_final: 0.7667 (m-30) REVERT: C 11 LYS cc_start: 0.9411 (mttp) cc_final: 0.9148 (mttt) REVERT: C 43 LYS cc_start: 0.8744 (mtpt) cc_final: 0.7913 (mtpp) REVERT: C 44 ASP cc_start: 0.7389 (m-30) cc_final: 0.6794 (m-30) REVERT: C 61 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: C 87 MET cc_start: 0.9026 (mtp) cc_final: 0.8791 (mtp) REVERT: C 114 ASN cc_start: 0.8833 (t0) cc_final: 0.8542 (t0) REVERT: D 44 ASP cc_start: 0.7656 (t0) cc_final: 0.7433 (t70) REVERT: D 58 SER cc_start: 0.8332 (m) cc_final: 0.8065 (p) REVERT: F 5 ASN cc_start: 0.8609 (t0) cc_final: 0.8385 (t0) REVERT: F 61 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: F 87 MET cc_start: 0.8954 (mtp) cc_final: 0.8740 (mtp) REVERT: G 53 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7471 (mp0) REVERT: G 102 GLU cc_start: 0.7571 (tm-30) cc_final: 0.6873 (tm-30) REVERT: H 135 GLU cc_start: 0.8402 (mp0) cc_final: 0.8188 (mp0) REVERT: I 20 TYR cc_start: 0.9040 (t80) cc_final: 0.8668 (t80) REVERT: I 38 ARG cc_start: 0.8988 (ttt180) cc_final: 0.8733 (ttt180) REVERT: I 43 LYS cc_start: 0.9067 (mtpt) cc_final: 0.7683 (mptt) REVERT: I 97 LEU cc_start: 0.9074 (mt) cc_final: 0.8816 (mt) REVERT: L 101 ASN cc_start: 0.8684 (m-40) cc_final: 0.8159 (m-40) outliers start: 35 outliers final: 30 residues processed: 272 average time/residue: 0.2951 time to fit residues: 112.5041 Evaluate side-chains 220 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 94 GLN F 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14520 Z= 0.307 Angle : 0.546 5.210 19800 Z= 0.289 Chirality : 0.046 0.154 2148 Planarity : 0.004 0.033 2580 Dihedral : 5.042 55.650 1984 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.67 % Allowed : 10.67 % Favored : 84.67 % 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: -0.78 (0.17), residues: 1824 helix: 1.46 (0.42), residues: 144 sheet: -0.42 (0.16), residues: 936 loop : -0.88 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 36 PHE 0.013 0.002 PHE J 120 TYR 0.015 0.002 TYR C 108 ARG 0.003 0.001 ARG I 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 191 time to evaluate : 1.544 Fit side-chains REVERT: A 134 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8969 (mtmt) REVERT: B 61 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: C 11 LYS cc_start: 0.9417 (mttp) cc_final: 0.9158 (mttt) REVERT: C 43 LYS cc_start: 0.8873 (mtpt) cc_final: 0.7992 (mtpp) REVERT: C 44 ASP cc_start: 0.7530 (m-30) cc_final: 0.6960 (m-30) REVERT: C 61 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: C 87 MET cc_start: 0.9258 (mtp) cc_final: 0.8947 (mtp) REVERT: G 53 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7503 (mp0) REVERT: G 102 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7034 (tm-30) REVERT: H 135 GLU cc_start: 0.8441 (mp0) cc_final: 0.8175 (mp0) REVERT: I 20 TYR cc_start: 0.9029 (t80) cc_final: 0.8616 (t80) REVERT: I 43 LYS cc_start: 0.8934 (mtpt) cc_final: 0.7566 (mptt) REVERT: K 118 ASP cc_start: 0.7804 (t0) cc_final: 0.7569 (t0) REVERT: K 135 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7539 (mp0) REVERT: L 59 TYR cc_start: 0.8594 (m-80) cc_final: 0.8390 (m-10) REVERT: L 101 ASN cc_start: 0.8652 (m-40) cc_final: 0.8175 (m-40) outliers start: 70 outliers final: 58 residues processed: 255 average time/residue: 0.2943 time to fit residues: 105.5312 Evaluate side-chains 242 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 182 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 0.0980 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 109 optimal weight: 0.1980 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 94 GLN F 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14520 Z= 0.133 Angle : 0.459 5.194 19800 Z= 0.239 Chirality : 0.043 0.150 2148 Planarity : 0.003 0.026 2580 Dihedral : 4.151 51.847 1982 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.53 % Allowed : 12.07 % Favored : 84.40 % 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: -0.57 (0.17), residues: 1824 helix: 1.70 (0.40), residues: 144 sheet: -0.29 (0.16), residues: 948 loop : -0.77 (0.16), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 36 PHE 0.008 0.001 PHE J 120 TYR 0.010 0.001 TYR C 108 ARG 0.004 0.000 ARG F 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 210 time to evaluate : 1.726 Fit side-chains REVERT: A 10 VAL cc_start: 0.9186 (p) cc_final: 0.8805 (m) REVERT: A 134 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8915 (mtmt) REVERT: B 61 ASP cc_start: 0.8166 (m-30) cc_final: 0.7714 (m-30) REVERT: B 97 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8645 (mt) REVERT: C 10 VAL cc_start: 0.9242 (p) cc_final: 0.8939 (m) REVERT: C 11 LYS cc_start: 0.9340 (mttp) cc_final: 0.9054 (mttt) REVERT: C 43 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8155 (mtpp) REVERT: C 61 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: C 87 MET cc_start: 0.9090 (mtp) cc_final: 0.8787 (mtp) REVERT: D 97 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8518 (mm) REVERT: F 10 VAL cc_start: 0.9238 (p) cc_final: 0.8819 (m) REVERT: G 53 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7496 (mp0) REVERT: H 135 GLU cc_start: 0.8292 (mp0) cc_final: 0.8044 (mp0) REVERT: I 38 ARG cc_start: 0.9045 (ttt180) cc_final: 0.8661 (ttt180) REVERT: I 43 LYS cc_start: 0.8837 (mtpt) cc_final: 0.7446 (mptt) REVERT: K 20 TYR cc_start: 0.9029 (t80) cc_final: 0.8822 (t80) REVERT: K 74 GLN cc_start: 0.8888 (tt0) cc_final: 0.8596 (tt0) REVERT: K 118 ASP cc_start: 0.7777 (t0) cc_final: 0.7524 (t0) REVERT: L 59 TYR cc_start: 0.8386 (m-80) cc_final: 0.8142 (m-10) REVERT: L 101 ASN cc_start: 0.8512 (m-40) cc_final: 0.8235 (m-40) outliers start: 53 outliers final: 40 residues processed: 254 average time/residue: 0.2936 time to fit residues: 104.8457 Evaluate side-chains 231 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 14520 Z= 0.580 Angle : 0.683 7.901 19800 Z= 0.361 Chirality : 0.051 0.175 2148 Planarity : 0.005 0.039 2580 Dihedral : 5.366 51.148 1982 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 6.47 % Allowed : 11.73 % Favored : 81.80 % 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: -0.98 (0.17), residues: 1824 helix: 1.25 (0.42), residues: 144 sheet: -0.54 (0.16), residues: 936 loop : -1.02 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP E 18 PHE 0.023 0.003 PHE C 120 TYR 0.014 0.003 TYR E 108 ARG 0.005 0.001 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 191 time to evaluate : 1.786 Fit side-chains REVERT: B 61 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: B 121 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.7998 (ttm-80) REVERT: C 11 LYS cc_start: 0.9415 (mttp) cc_final: 0.9187 (mttt) REVERT: C 87 MET cc_start: 0.9394 (mtp) cc_final: 0.9060 (mtp) REVERT: D 97 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8765 (mm) REVERT: F 8 MET cc_start: 0.8166 (mmm) cc_final: 0.7589 (mtm) REVERT: F 114 ASN cc_start: 0.8954 (t0) cc_final: 0.8654 (t0) REVERT: G 53 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7599 (mp0) REVERT: H 29 ASN cc_start: 0.9325 (t0) cc_final: 0.9069 (t0) REVERT: I 43 LYS cc_start: 0.9014 (mtpt) cc_final: 0.7554 (mptt) REVERT: J 153 GLU cc_start: 0.8614 (pm20) cc_final: 0.8225 (pm20) outliers start: 97 outliers final: 75 residues processed: 278 average time/residue: 0.2924 time to fit residues: 115.8468 Evaluate side-chains 257 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 180 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14520 Z= 0.148 Angle : 0.474 5.629 19800 Z= 0.247 Chirality : 0.044 0.155 2148 Planarity : 0.003 0.032 2580 Dihedral : 4.301 50.888 1982 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 4.53 % Allowed : 14.07 % Favored : 81.40 % 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: -0.73 (0.17), residues: 1824 helix: 0.99 (0.39), residues: 156 sheet: -0.36 (0.16), residues: 948 loop : -0.82 (0.17), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 36 PHE 0.008 0.001 PHE J 120 TYR 0.009 0.001 TYR B 108 ARG 0.004 0.000 ARG F 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 195 time to evaluate : 1.588 Fit side-chains REVERT: B 61 ASP cc_start: 0.8074 (m-30) cc_final: 0.7740 (m-30) REVERT: B 97 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8608 (mt) REVERT: C 11 LYS cc_start: 0.9369 (mttp) cc_final: 0.9100 (mttt) REVERT: C 61 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: C 87 MET cc_start: 0.9195 (mtp) cc_final: 0.8903 (mtp) REVERT: F 8 MET cc_start: 0.8147 (mmm) cc_final: 0.7620 (mtm) REVERT: F 10 VAL cc_start: 0.9213 (p) cc_final: 0.8874 (m) REVERT: G 53 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7532 (mp0) REVERT: H 57 ASP cc_start: 0.8042 (t0) cc_final: 0.7828 (t0) REVERT: H 135 GLU cc_start: 0.8327 (mp0) cc_final: 0.8043 (mp0) REVERT: I 43 LYS cc_start: 0.8857 (mtpt) cc_final: 0.7496 (mptt) REVERT: K 74 GLN cc_start: 0.8955 (tt0) cc_final: 0.8678 (tt0) REVERT: L 101 ASN cc_start: 0.8564 (m-40) cc_final: 0.8244 (m-40) outliers start: 68 outliers final: 56 residues processed: 253 average time/residue: 0.2839 time to fit residues: 102.5026 Evaluate side-chains 237 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 179 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.0670 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 overall best weight: 3.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14520 Z= 0.355 Angle : 0.568 6.696 19800 Z= 0.299 Chirality : 0.047 0.165 2148 Planarity : 0.004 0.036 2580 Dihedral : 4.862 50.613 1982 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.80 % Allowed : 13.73 % Favored : 80.47 % 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: -0.82 (0.17), residues: 1824 helix: 0.94 (0.40), residues: 156 sheet: -0.43 (0.16), residues: 936 loop : -0.84 (0.17), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 36 PHE 0.016 0.002 PHE C 120 TYR 0.013 0.002 TYR C 108 ARG 0.004 0.000 ARG F 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 185 time to evaluate : 1.205 Fit side-chains REVERT: C 11 LYS cc_start: 0.9396 (mttp) cc_final: 0.9168 (mttt) REVERT: C 61 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: F 8 MET cc_start: 0.8173 (mmm) cc_final: 0.7604 (mtm) REVERT: F 10 VAL cc_start: 0.9273 (p) cc_final: 0.8876 (m) REVERT: G 53 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7580 (mp0) REVERT: I 20 TYR cc_start: 0.8954 (t80) cc_final: 0.8534 (t80) REVERT: I 43 LYS cc_start: 0.8948 (mtpt) cc_final: 0.7682 (mptt) REVERT: J 101 ASN cc_start: 0.8517 (m-40) cc_final: 0.8305 (m110) REVERT: L 43 LYS cc_start: 0.9084 (mtpt) cc_final: 0.7926 (mptt) REVERT: L 101 ASN cc_start: 0.8643 (m-40) cc_final: 0.8229 (m-40) REVERT: L 153 GLU cc_start: 0.8712 (pm20) cc_final: 0.8370 (pm20) outliers start: 87 outliers final: 76 residues processed: 261 average time/residue: 0.2719 time to fit residues: 100.0850 Evaluate side-chains 257 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 180 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.0370 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 29 ASN J 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14520 Z= 0.132 Angle : 0.466 5.608 19800 Z= 0.240 Chirality : 0.043 0.156 2148 Planarity : 0.003 0.030 2580 Dihedral : 4.070 49.093 1982 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 4.47 % Allowed : 15.07 % Favored : 80.47 % 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: -0.60 (0.17), residues: 1824 helix: 1.18 (0.38), residues: 156 sheet: -0.27 (0.16), residues: 948 loop : -0.77 (0.17), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 36 PHE 0.009 0.001 PHE K 120 TYR 0.009 0.001 TYR B 108 ARG 0.005 0.000 ARG F 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 198 time to evaluate : 1.618 Fit side-chains REVERT: A 10 VAL cc_start: 0.9210 (p) cc_final: 0.8829 (m) REVERT: B 61 ASP cc_start: 0.8021 (m-30) cc_final: 0.7449 (m-30) REVERT: B 118 ASP cc_start: 0.8364 (m-30) cc_final: 0.7854 (m-30) REVERT: C 10 VAL cc_start: 0.9251 (p) cc_final: 0.8917 (m) REVERT: C 11 LYS cc_start: 0.9321 (mttp) cc_final: 0.9026 (mttt) REVERT: C 61 ASP cc_start: 0.8326 (t0) cc_final: 0.8095 (m-30) REVERT: F 8 MET cc_start: 0.8163 (mmm) cc_final: 0.7616 (mtm) REVERT: F 10 VAL cc_start: 0.9241 (p) cc_final: 0.8888 (m) REVERT: G 53 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7548 (mp0) REVERT: H 57 ASP cc_start: 0.7993 (t0) cc_final: 0.7758 (t0) REVERT: H 135 GLU cc_start: 0.8288 (mp0) cc_final: 0.7985 (mp0) REVERT: I 20 TYR cc_start: 0.8993 (t80) cc_final: 0.8504 (t80) REVERT: I 43 LYS cc_start: 0.8815 (mtpt) cc_final: 0.7519 (mptt) REVERT: K 42 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8383 (p) REVERT: K 74 GLN cc_start: 0.8921 (tt0) cc_final: 0.8627 (tt0) REVERT: L 43 LYS cc_start: 0.9051 (mtpt) cc_final: 0.7698 (mptt) REVERT: L 101 ASN cc_start: 0.8488 (m-40) cc_final: 0.8272 (m-40) outliers start: 67 outliers final: 58 residues processed: 254 average time/residue: 0.2723 time to fit residues: 99.0326 Evaluate side-chains 244 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 185 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 101 ASN J 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 14520 Z= 0.447 Angle : 0.617 7.060 19800 Z= 0.324 Chirality : 0.048 0.169 2148 Planarity : 0.004 0.036 2580 Dihedral : 4.850 17.682 1980 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.33 % Allowed : 14.27 % Favored : 80.40 % 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: -0.87 (0.17), residues: 1824 helix: 0.90 (0.40), residues: 156 sheet: -0.44 (0.16), residues: 936 loop : -0.91 (0.17), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 18 PHE 0.019 0.002 PHE C 120 TYR 0.015 0.002 TYR E 108 ARG 0.005 0.001 ARG J 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 183 time to evaluate : 1.760 Fit side-chains REVERT: B 118 ASP cc_start: 0.8425 (m-30) cc_final: 0.8066 (m-30) REVERT: C 11 LYS cc_start: 0.9392 (mttp) cc_final: 0.9165 (mttt) REVERT: C 61 ASP cc_start: 0.8236 (t0) cc_final: 0.8015 (t70) REVERT: F 8 MET cc_start: 0.8157 (mmm) cc_final: 0.7627 (mtm) REVERT: F 10 VAL cc_start: 0.9289 (p) cc_final: 0.8898 (m) REVERT: G 53 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7573 (mp0) REVERT: I 20 TYR cc_start: 0.8957 (t80) cc_final: 0.8736 (t80) REVERT: I 43 LYS cc_start: 0.8965 (mtpt) cc_final: 0.7621 (mptt) REVERT: L 43 LYS cc_start: 0.9094 (mtpt) cc_final: 0.7929 (mptt) REVERT: L 153 GLU cc_start: 0.8804 (pm20) cc_final: 0.8451 (pm20) outliers start: 80 outliers final: 72 residues processed: 256 average time/residue: 0.2726 time to fit residues: 99.5758 Evaluate side-chains 250 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 178 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 153 GLU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14520 Z= 0.211 Angle : 0.510 6.190 19800 Z= 0.266 Chirality : 0.044 0.157 2148 Planarity : 0.003 0.034 2580 Dihedral : 4.324 16.976 1980 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.53 % Allowed : 15.20 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 1824 helix: 1.05 (0.39), residues: 156 sheet: -0.38 (0.16), residues: 936 loop : -0.82 (0.18), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 PHE 0.011 0.001 PHE J 120 TYR 0.012 0.001 TYR C 108 ARG 0.005 0.000 ARG F 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 183 time to evaluate : 1.506 Fit side-chains REVERT: B 118 ASP cc_start: 0.8436 (m-30) cc_final: 0.8008 (m-30) REVERT: C 11 LYS cc_start: 0.9375 (mttp) cc_final: 0.9119 (mttt) REVERT: C 61 ASP cc_start: 0.8185 (t0) cc_final: 0.7914 (m-30) REVERT: F 8 MET cc_start: 0.8177 (mmm) cc_final: 0.7559 (mtm) REVERT: F 10 VAL cc_start: 0.9256 (p) cc_final: 0.8900 (m) REVERT: G 53 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7553 (mp0) REVERT: H 57 ASP cc_start: 0.8111 (t0) cc_final: 0.7826 (t0) REVERT: I 20 TYR cc_start: 0.8922 (t80) cc_final: 0.8510 (t80) REVERT: I 43 LYS cc_start: 0.8793 (mtpt) cc_final: 0.7519 (mptt) REVERT: L 43 LYS cc_start: 0.9080 (mtpt) cc_final: 0.7924 (mptt) REVERT: L 101 ASN cc_start: 0.8580 (m-40) cc_final: 0.8251 (m-40) REVERT: L 153 GLU cc_start: 0.8741 (pm20) cc_final: 0.8414 (pm20) outliers start: 68 outliers final: 67 residues processed: 243 average time/residue: 0.2755 time to fit residues: 95.7430 Evaluate side-chains 249 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 182 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.087932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.073191 restraints weight = 20672.410| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 1.63 r_work: 0.2524 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2393 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14520 Z= 0.200 Angle : 0.502 6.040 19800 Z= 0.261 Chirality : 0.044 0.157 2148 Planarity : 0.003 0.036 2580 Dihedral : 4.176 16.773 1980 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.00 % Allowed : 14.87 % Favored : 80.13 % 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: -0.75 (0.17), residues: 1824 helix: 1.24 (0.39), residues: 156 sheet: -0.37 (0.16), residues: 948 loop : -0.89 (0.18), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 PHE 0.011 0.001 PHE J 120 TYR 0.011 0.001 TYR C 108 ARG 0.007 0.000 ARG F 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2952.58 seconds wall clock time: 56 minutes 25.47 seconds (3385.47 seconds total)