Starting phenix.real_space_refine on Sat Mar 7 10:56:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wr2_21875/03_2026/6wr2_21875.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wr2_21875/03_2026/6wr2_21875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wr2_21875/03_2026/6wr2_21875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wr2_21875/03_2026/6wr2_21875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wr2_21875/03_2026/6wr2_21875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wr2_21875/03_2026/6wr2_21875.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 168 5.16 5 C 13445 2.51 5 N 3675 2.21 5 O 4022 1.98 5 H 21361 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42671 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "h" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 2944 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 1 Chain: "i" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "j" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 2956 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 1 Chain: "k" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2976 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "l" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "m" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2971 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "n" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3017 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "M" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3105 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "H" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.51, per 1000 atoms: 0.18 Number of scatterers: 42671 At special positions: 0 Unit cell: (112.23, 113.1, 125.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 O 4022 8.00 N 3675 7.00 C 13445 6.00 H 21361 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5010 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 49 sheets defined 49.5% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.537A pdb=" N GLU h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 54 Processing helix chain 'h' and resid 69 through 83 removed outlier: 3.567A pdb=" N GLY h 73 " --> pdb=" O VAL h 69 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 105 Processing helix chain 'h' and resid 132 through 158 Processing helix chain 'h' and resid 160 through 169 Processing helix chain 'h' and resid 176 through 183 Processing helix chain 'i' and resid 19 through 26 removed outlier: 3.779A pdb=" N GLU i 26 " --> pdb=" O ARG i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 54 Processing helix chain 'i' and resid 69 through 83 removed outlier: 3.658A pdb=" N GLY i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 105 Processing helix chain 'i' and resid 132 through 158 Processing helix chain 'i' and resid 160 through 169 Processing helix chain 'i' and resid 176 through 182 Processing helix chain 'j' and resid 19 through 25 Processing helix chain 'j' and resid 36 through 54 Processing helix chain 'j' and resid 69 through 83 removed outlier: 3.606A pdb=" N GLY j 73 " --> pdb=" O VAL j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 105 Processing helix chain 'j' and resid 132 through 158 Processing helix chain 'j' and resid 160 through 169 Processing helix chain 'j' and resid 176 through 182 Processing helix chain 'k' and resid 19 through 25 Processing helix chain 'k' and resid 36 through 54 Processing helix chain 'k' and resid 69 through 83 removed outlier: 3.677A pdb=" N GLY k 73 " --> pdb=" O VAL k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 105 Processing helix chain 'k' and resid 132 through 158 Processing helix chain 'k' and resid 160 through 169 Processing helix chain 'k' and resid 176 through 182 Processing helix chain 'l' and resid 19 through 25 Processing helix chain 'l' and resid 36 through 54 Processing helix chain 'l' and resid 69 through 83 removed outlier: 3.770A pdb=" N GLY l 73 " --> pdb=" O VAL l 69 " (cutoff:3.500A) Processing helix chain 'l' and resid 96 through 105 Processing helix chain 'l' and resid 132 through 158 Processing helix chain 'l' and resid 160 through 169 Processing helix chain 'l' and resid 176 through 182 Processing helix chain 'm' and resid 19 through 26 removed outlier: 3.875A pdb=" N GLU m 26 " --> pdb=" O ARG m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 54 Processing helix chain 'm' and resid 69 through 83 removed outlier: 3.594A pdb=" N GLY m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 105 Processing helix chain 'm' and resid 132 through 158 Processing helix chain 'm' and resid 160 through 169 Processing helix chain 'm' and resid 176 through 183 Processing helix chain 'n' and resid 19 through 26 removed outlier: 3.550A pdb=" N GLU n 26 " --> pdb=" O ARG n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 54 Processing helix chain 'n' and resid 69 through 83 removed outlier: 3.588A pdb=" N GLY n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 96 through 105 Processing helix chain 'n' and resid 132 through 158 Processing helix chain 'n' and resid 160 through 169 Processing helix chain 'n' and resid 176 through 182 Processing helix chain 'n' and resid 191 through 196 Processing helix chain 'M' and resid 19 through 25 Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.644A pdb=" N GLY M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 132 through 158 Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'N' and resid 19 through 25 Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 70 through 83 removed outlier: 3.683A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 105 Processing helix chain 'N' and resid 132 through 158 Processing helix chain 'N' and resid 160 through 169 Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'N' and resid 191 through 196 removed outlier: 3.654A pdb=" N ASN N 195 " --> pdb=" O HIS N 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.540A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.726A pdb=" N GLY H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 132 through 158 Processing helix chain 'H' and resid 160 through 169 Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'I' and resid 19 through 26 Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.665A pdb=" N GLY I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 132 through 158 Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 25 Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.630A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 132 through 158 Processing helix chain 'J' and resid 160 through 169 Processing helix chain 'J' and resid 176 through 183 Processing helix chain 'K' and resid 19 through 25 Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 70 through 83 removed outlier: 3.696A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 105 Processing helix chain 'K' and resid 132 through 158 Processing helix chain 'K' and resid 160 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.551A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 70 through 83 removed outlier: 3.660A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 105 Processing helix chain 'L' and resid 132 through 158 Processing helix chain 'L' and resid 160 through 169 Processing helix chain 'L' and resid 176 through 183 Processing sheet with id=AA1, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.338A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG h 118 " --> pdb=" O CYS h 91 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY h 93 " --> pdb=" O ARG h 118 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N MET h 120 " --> pdb=" O GLY h 93 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA h 95 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.338A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE h 112 " --> pdb=" O VAL h 87 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR h 89 " --> pdb=" O PHE h 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 125 through 131 Processing sheet with id=AA5, first strand: chain 'i' and resid 5 through 8 Processing sheet with id=AA6, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.355A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG i 118 " --> pdb=" O CYS i 91 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY i 93 " --> pdb=" O ARG i 118 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N MET i 120 " --> pdb=" O GLY i 93 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA i 95 " --> pdb=" O MET i 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.355A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE i 112 " --> pdb=" O VAL i 87 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR i 89 " --> pdb=" O PHE i 112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER i 187 " --> pdb=" O ARG i 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'i' and resid 125 through 131 Processing sheet with id=AA9, first strand: chain 'j' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.316A pdb=" N ILE j 59 " --> pdb=" O SER j 88 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE j 90 " --> pdb=" O ILE j 59 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU j 61 " --> pdb=" O ILE j 90 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N MET j 92 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE j 63 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN j 94 " --> pdb=" O ILE j 63 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE j 112 " --> pdb=" O VAL j 87 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR j 89 " --> pdb=" O PHE j 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'j' and resid 118 through 121 Processing sheet with id=AB3, first strand: chain 'j' and resid 125 through 131 Processing sheet with id=AB4, first strand: chain 'k' and resid 5 through 8 removed outlier: 4.119A pdb=" N GLU k 8 " --> pdb=" O ARG k 15 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG k 15 " --> pdb=" O GLU k 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.395A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE k 112 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR k 89 " --> pdb=" O PHE k 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER k 187 " --> pdb=" O ARG k 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'k' and resid 118 through 121 Processing sheet with id=AB7, first strand: chain 'k' and resid 125 through 131 Processing sheet with id=AB8, first strand: chain 'l' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.428A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG l 118 " --> pdb=" O CYS l 91 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY l 93 " --> pdb=" O ARG l 118 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N MET l 120 " --> pdb=" O GLY l 93 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA l 95 " --> pdb=" O MET l 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.428A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE l 112 " --> pdb=" O VAL l 87 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR l 89 " --> pdb=" O PHE l 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'l' and resid 125 through 131 Processing sheet with id=AC3, first strand: chain 'm' and resid 5 through 7 Processing sheet with id=AC4, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.465A pdb=" N ILE m 59 " --> pdb=" O SER m 88 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE m 90 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU m 61 " --> pdb=" O ILE m 90 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N MET m 92 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE m 63 " --> pdb=" O MET m 92 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN m 94 " --> pdb=" O ILE m 63 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE m 112 " --> pdb=" O VAL m 87 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR m 89 " --> pdb=" O PHE m 112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'm' and resid 118 through 121 Processing sheet with id=AC6, first strand: chain 'm' and resid 125 through 131 Processing sheet with id=AC7, first strand: chain 'n' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.308A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG n 118 " --> pdb=" O CYS n 91 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY n 93 " --> pdb=" O ARG n 118 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N MET n 120 " --> pdb=" O GLY n 93 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA n 95 " --> pdb=" O MET n 120 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.308A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE n 112 " --> pdb=" O VAL n 87 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR n 89 " --> pdb=" O PHE n 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'n' and resid 125 through 131 Processing sheet with id=AD2, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AD3, first strand: chain 'M' and resid 28 through 32 removed outlier: 5.294A pdb=" N SER M 65 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN M 94 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG M 118 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY M 93 " --> pdb=" O ARG M 118 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N MET M 120 " --> pdb=" O GLY M 93 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA M 95 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 28 through 32 removed outlier: 5.294A pdb=" N SER M 65 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN M 94 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AD6, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.245A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG N 118 " --> pdb=" O CYS N 91 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY N 93 " --> pdb=" O ARG N 118 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N MET N 120 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA N 95 " --> pdb=" O MET N 120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.245A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER N 187 " --> pdb=" O ARG N 111 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS N 113 " --> pdb=" O SER N 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AD9, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.643A pdb=" N ILE H 29 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN H 64 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU H 31 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG H 118 " --> pdb=" O CYS H 91 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLY H 93 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N MET H 120 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA H 95 " --> pdb=" O MET H 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.643A pdb=" N ILE H 29 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN H 64 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU H 31 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 5 through 8 Processing sheet with id=AE3, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.319A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N MET I 120 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.319A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER I 187 " --> pdb=" O ARG I 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 5 through 8 Processing sheet with id=AE6, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.664A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY J 93 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N MET J 120 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.664A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AE9, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.299A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG K 118 " --> pdb=" O CYS K 91 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY K 93 " --> pdb=" O ARG K 118 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N MET K 120 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.299A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER K 187 " --> pdb=" O ARG K 111 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AF3, first strand: chain 'L' and resid 28 through 32 removed outlier: 5.257A pdb=" N SER L 65 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLN L 94 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG L 118 " --> pdb=" O CYS L 91 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY L 93 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N MET L 120 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 28 through 32 removed outlier: 5.257A pdb=" N SER L 65 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLN L 94 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) 1211 hydrogen bonds defined for protein. 3561 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: 11.79 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 21333 1.03 - 1.22: 68 1.22 - 1.42: 8790 1.42 - 1.62: 12491 1.62 - 1.82: 308 Bond restraints: 42990 Sorted by residual: bond pdb=" CA LEU M 189 " pdb=" CB LEU M 189 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.76e-02 3.23e+03 7.55e+00 bond pdb=" CA ALA M 96 " pdb=" CB ALA M 96 " ideal model delta sigma weight residual 1.527 1.489 0.038 1.49e-02 4.50e+03 6.52e+00 bond pdb=" CG1 ILE L 63 " pdb=" CD1 ILE L 63 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.50e+00 bond pdb=" CG1 ILE M 63 " pdb=" CD1 ILE M 63 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.46e+00 bond pdb=" CG1 ILE N 63 " pdb=" CD1 ILE N 63 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.37e+00 ... (remaining 42985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 74508 1.70 - 3.39: 2848 3.39 - 5.09: 313 5.09 - 6.79: 49 6.79 - 8.48: 13 Bond angle restraints: 77731 Sorted by residual: angle pdb=" N SER M 65 " pdb=" CA SER M 65 " pdb=" C SER M 65 " ideal model delta sigma weight residual 109.64 115.61 -5.97 1.56e+00 4.11e-01 1.47e+01 angle pdb=" N ASP K 18 " pdb=" CA ASP K 18 " pdb=" C ASP K 18 " ideal model delta sigma weight residual 110.55 106.07 4.48 1.35e+00 5.49e-01 1.10e+01 angle pdb=" C PHE N 17 " pdb=" CA PHE N 17 " pdb=" CB PHE N 17 " ideal model delta sigma weight residual 109.56 102.34 7.22 2.22e+00 2.03e-01 1.06e+01 angle pdb=" N ASP I 18 " pdb=" CA ASP I 18 " pdb=" C ASP I 18 " ideal model delta sigma weight residual 110.55 106.17 4.38 1.35e+00 5.49e-01 1.05e+01 angle pdb=" N ASP J 18 " pdb=" CA ASP J 18 " pdb=" C ASP J 18 " ideal model delta sigma weight residual 110.55 106.30 4.25 1.35e+00 5.49e-01 9.93e+00 ... (remaining 77726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 17734 17.62 - 35.23: 1722 35.23 - 52.85: 481 52.85 - 70.47: 125 70.47 - 88.08: 11 Dihedral angle restraints: 20073 sinusoidal: 11191 harmonic: 8882 Sorted by residual: dihedral pdb=" CB MET I 120 " pdb=" CG MET I 120 " pdb=" SD MET I 120 " pdb=" CE MET I 120 " ideal model delta sinusoidal sigma weight residual 60.00 117.36 -57.36 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB MET H 120 " pdb=" CG MET H 120 " pdb=" SD MET H 120 " pdb=" CE MET H 120 " ideal model delta sinusoidal sigma weight residual 180.00 122.97 57.03 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CB MET j 120 " pdb=" CG MET j 120 " pdb=" SD MET j 120 " pdb=" CE MET j 120 " ideal model delta sinusoidal sigma weight residual 60.00 112.44 -52.44 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 20070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1770 0.041 - 0.083: 960 0.083 - 0.124: 473 0.124 - 0.165: 78 0.165 - 0.207: 21 Chirality restraints: 3302 Sorted by residual: chirality pdb=" CA PRO j 115 " pdb=" N PRO j 115 " pdb=" C PRO j 115 " pdb=" CB PRO j 115 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PRO k 115 " pdb=" N PRO k 115 " pdb=" C PRO k 115 " pdb=" CB PRO k 115 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL i 185 " pdb=" CA VAL i 185 " pdb=" CG1 VAL i 185 " pdb=" CG2 VAL i 185 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3299 not shown) Planarity restraints: 6387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO M 66 " -0.029 2.00e-02 2.50e+03 5.72e-02 3.28e+01 pdb=" C PRO M 66 " 0.099 2.00e-02 2.50e+03 pdb=" O PRO M 66 " -0.036 2.00e-02 2.50e+03 pdb=" N GLY M 67 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 12 " -0.307 9.50e-02 1.11e+02 1.02e-01 1.11e+01 pdb=" NE ARG I 12 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG I 12 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG I 12 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG I 12 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG I 12 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG I 12 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG I 12 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG I 12 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 118 " -0.286 9.50e-02 1.11e+02 9.55e-02 9.68e+00 pdb=" NE ARG H 118 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG H 118 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 118 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 118 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG H 118 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG H 118 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG H 118 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG H 118 " -0.005 2.00e-02 2.50e+03 ... (remaining 6384 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 5256 2.24 - 2.83: 98910 2.83 - 3.42: 110512 3.42 - 4.01: 162083 4.01 - 4.60: 256374 Nonbonded interactions: 633135 Sorted by model distance: nonbonded pdb=" HG1 THR M 10 " pdb=" O GLY M 13 " model vdw 1.649 2.450 nonbonded pdb=" HG1 THR N 10 " pdb=" O GLY N 13 " model vdw 1.653 2.450 nonbonded pdb=" O MET K 153 " pdb=" HG1 THR K 157 " model vdw 1.681 2.450 nonbonded pdb=" O MET M 153 " pdb=" HG1 THR M 157 " model vdw 1.684 2.450 nonbonded pdb=" O ALA m 72 " pdb=" HG SER m 75 " model vdw 1.685 2.450 ... (remaining 633130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'H' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'I' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'J' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'K' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'L' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'M' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'N' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'h' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 through 16 or (resid 17 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HZ )) or resid 18 through 191 or (resid 192 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e NE or name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or na \ me HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 \ or name HH21 or name HH22)) or resid 193)) selection = (chain 'i' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'j' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'k' and (resid 2 through 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD \ 2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) o \ r resid 193)) selection = (chain 'l' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 193)) selection = (chain 'm' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 193)) selection = (chain 'n' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) } 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: 4.430 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: 0.250 Extract box with map and model: 0.600 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 39.690 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 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: 0.020 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 : 0.014 0.095 21629 Z= 0.566 Angle : 0.878 8.483 29139 Z= 0.474 Chirality : 0.059 0.207 3302 Planarity : 0.006 0.132 3789 Dihedral : 12.474 88.083 8173 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 2675 helix: 1.12 (0.14), residues: 1389 sheet: 0.11 (0.26), residues: 292 loop : -1.78 (0.16), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 15 TYR 0.013 0.002 TYR m 62 PHE 0.042 0.002 PHE N 17 HIS 0.011 0.003 HIS K 122 Details of bonding type rmsd covalent geometry : bond 0.01448 (21629) covalent geometry : angle 0.87761 (29139) hydrogen bonds : bond 0.20285 ( 1156) hydrogen bonds : angle 6.31703 ( 3561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 57 LYS cc_start: 0.7174 (mtpp) cc_final: 0.6771 (mtmt) REVERT: h 129 GLN cc_start: 0.7592 (mt0) cc_final: 0.6848 (mm-40) REVERT: h 191 HIS cc_start: 0.7493 (m90) cc_final: 0.7211 (m-70) REVERT: i 21 SER cc_start: 0.7320 (m) cc_final: 0.6689 (m) REVERT: i 22 ARG cc_start: 0.7594 (tpt90) cc_final: 0.7146 (tpt90) REVERT: j 151 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6313 (mt-10) REVERT: k 26 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6347 (mt-10) REVERT: k 41 ASN cc_start: 0.7009 (t0) cc_final: 0.6797 (t0) REVERT: l 108 LYS cc_start: 0.7572 (tptm) cc_final: 0.7154 (tppt) REVERT: l 168 THR cc_start: 0.5356 (p) cc_final: 0.5132 (p) REVERT: l 169 GLU cc_start: 0.6374 (mm-30) cc_final: 0.5934 (tm-30) REVERT: M 118 ARG cc_start: 0.7103 (mtt-85) cc_final: 0.6073 (ptp-170) REVERT: M 186 ASP cc_start: 0.7701 (m-30) cc_final: 0.7394 (m-30) REVERT: I 57 LYS cc_start: 0.7313 (mtpp) cc_final: 0.6942 (ttmt) REVERT: I 118 ARG cc_start: 0.7074 (mmt180) cc_final: 0.5850 (ttp-170) REVERT: J 57 LYS cc_start: 0.6867 (mtpp) cc_final: 0.6605 (ttpt) REVERT: J 118 ARG cc_start: 0.6631 (mmt180) cc_final: 0.6195 (ttm170) REVERT: K 84 LYS cc_start: 0.7504 (mtpt) cc_final: 0.7026 (mmpt) REVERT: K 118 ARG cc_start: 0.6798 (mtt-85) cc_final: 0.5877 (ptt180) REVERT: L 56 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7004 (mp0) REVERT: L 117 SER cc_start: 0.8098 (p) cc_final: 0.7540 (m) REVERT: L 118 ARG cc_start: 0.6931 (mtt-85) cc_final: 0.5950 (ptm160) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 1.3644 time to fit residues: 846.8114 Evaluate side-chains 399 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 41 ASN i 41 ASN j 41 ASN j 81 GLN l 129 GLN l 159 GLN m 159 GLN n 41 ASN M 41 ASN N 41 ASN N 159 GLN H 41 ASN I 41 ASN J 41 ASN J 123 GLN J 129 GLN K 41 ASN L 9 GLN L 41 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.157636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142990 restraints weight = 64732.380| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.54 r_work: 0.3687 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21629 Z= 0.146 Angle : 0.537 6.059 29139 Z= 0.281 Chirality : 0.042 0.191 3302 Planarity : 0.004 0.041 3789 Dihedral : 3.773 22.776 2949 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.31 % Allowed : 10.88 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 2675 helix: 1.78 (0.14), residues: 1389 sheet: -0.19 (0.29), residues: 273 loop : -1.18 (0.17), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 15 TYR 0.013 0.001 TYR k 77 PHE 0.018 0.001 PHE m 101 HIS 0.006 0.001 HIS k 191 Details of bonding type rmsd covalent geometry : bond 0.00326 (21629) covalent geometry : angle 0.53687 (29139) hydrogen bonds : bond 0.03778 ( 1156) hydrogen bonds : angle 4.30405 ( 3561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 497 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 57 LYS cc_start: 0.7627 (mtpp) cc_final: 0.7355 (mtmt) REVERT: h 129 GLN cc_start: 0.8340 (mt0) cc_final: 0.7987 (mp10) REVERT: h 191 HIS cc_start: 0.7725 (m90) cc_final: 0.7490 (m-70) REVERT: i 22 ARG cc_start: 0.8192 (tpt90) cc_final: 0.7934 (tpt90) REVERT: i 118 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7840 (mtp85) REVERT: i 151 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7200 (mt-10) REVERT: j 41 ASN cc_start: 0.7792 (t0) cc_final: 0.7353 (t0) REVERT: j 181 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7310 (mp0) REVERT: k 26 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6391 (tp30) REVERT: l 5 MET cc_start: 0.6521 (mpt) cc_final: 0.6213 (mpp) REVERT: l 108 LYS cc_start: 0.8030 (tptm) cc_final: 0.7693 (tppt) REVERT: l 169 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6564 (tm-30) REVERT: m 108 LYS cc_start: 0.7430 (tptm) cc_final: 0.6891 (mppt) REVERT: m 118 ARG cc_start: 0.6949 (mtt-85) cc_final: 0.6601 (ptt180) REVERT: n 129 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7899 (mp10) REVERT: M 118 ARG cc_start: 0.7739 (mtt-85) cc_final: 0.6907 (ptt180) REVERT: M 166 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7867 (mtm-85) REVERT: M 186 ASP cc_start: 0.8571 (m-30) cc_final: 0.8293 (m-30) REVERT: I 57 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7713 (ttmt) REVERT: J 25 LYS cc_start: 0.7827 (tttm) cc_final: 0.7599 (ttpp) REVERT: K 15 ARG cc_start: 0.6950 (ttm170) cc_final: 0.6064 (ttm170) REVERT: K 57 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7514 (ttpt) REVERT: K 84 LYS cc_start: 0.8371 (mtpt) cc_final: 0.8044 (mmpt) REVERT: K 118 ARG cc_start: 0.7414 (mtt-85) cc_final: 0.6862 (ptt180) REVERT: L 54 ASN cc_start: 0.7940 (t0) cc_final: 0.7675 (t0) REVERT: L 118 ARG cc_start: 0.7693 (mtt-85) cc_final: 0.6942 (ptt180) REVERT: L 144 LYS cc_start: 0.8107 (mttt) cc_final: 0.7841 (mttp) outliers start: 30 outliers final: 10 residues processed: 510 average time/residue: 1.3980 time to fit residues: 806.6335 Evaluate side-chains 432 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 422 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain L residue 153 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 110 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 41 ASN i 41 ASN k 41 ASN l 41 ASN l 123 GLN l 129 GLN m 116 ASN n 195 ASN M 34 GLN M 123 GLN N 41 ASN N 129 GLN J 41 ASN K 123 GLN L 9 GLN L 123 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.106918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.091636 restraints weight = 67442.984| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.29 r_work: 0.2954 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 21629 Z= 0.280 Angle : 0.625 5.832 29139 Z= 0.338 Chirality : 0.046 0.172 3302 Planarity : 0.005 0.040 3789 Dihedral : 4.360 22.950 2949 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.35 % Allowed : 12.63 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2675 helix: 1.52 (0.14), residues: 1376 sheet: -0.45 (0.29), residues: 266 loop : -0.94 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 192 TYR 0.015 0.002 TYR N 62 PHE 0.018 0.002 PHE k 101 HIS 0.011 0.002 HIS k 191 Details of bonding type rmsd covalent geometry : bond 0.00669 (21629) covalent geometry : angle 0.62480 (29139) hydrogen bonds : bond 0.05702 ( 1156) hydrogen bonds : angle 4.48419 ( 3561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 531 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 57 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8158 (mtmt) REVERT: h 92 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8236 (ptt) REVERT: h 108 LYS cc_start: 0.8298 (tptm) cc_final: 0.7862 (mmtm) REVERT: h 129 GLN cc_start: 0.8462 (mt0) cc_final: 0.8244 (mm110) REVERT: i 22 ARG cc_start: 0.8406 (tpt90) cc_final: 0.8150 (tpt90) REVERT: i 118 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8163 (mtp85) REVERT: i 144 LYS cc_start: 0.8527 (mttt) cc_final: 0.8307 (mttt) REVERT: j 26 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7368 (mt-10) REVERT: j 41 ASN cc_start: 0.8211 (t0) cc_final: 0.7836 (t0) REVERT: j 144 LYS cc_start: 0.8621 (mttt) cc_final: 0.8098 (mttp) REVERT: k 26 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7535 (mm-30) REVERT: l 144 LYS cc_start: 0.8472 (ttmm) cc_final: 0.7954 (mtmt) REVERT: m 25 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7989 (mtpm) REVERT: m 43 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8696 (mt) REVERT: m 94 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: m 118 ARG cc_start: 0.7815 (mtt-85) cc_final: 0.7019 (ptt180) REVERT: m 153 MET cc_start: 0.8746 (mmt) cc_final: 0.8365 (mmt) REVERT: n 22 ARG cc_start: 0.8056 (tpt90) cc_final: 0.7846 (tpt90) REVERT: n 92 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8281 (ptt) REVERT: n 108 LYS cc_start: 0.8749 (tptm) cc_final: 0.8293 (mmtm) REVERT: n 140 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7875 (mtm-85) REVERT: M 14 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5211 (tt0) REVERT: M 118 ARG cc_start: 0.7911 (mtt-85) cc_final: 0.7204 (ptt180) REVERT: N 22 ARG cc_start: 0.8802 (tpt90) cc_final: 0.8159 (tpm-80) REVERT: N 34 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8283 (tp40) REVERT: N 41 ASN cc_start: 0.7750 (m-40) cc_final: 0.7490 (m110) REVERT: N 57 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8747 (mttt) REVERT: N 143 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8392 (mm) REVERT: N 148 ARG cc_start: 0.8153 (tpt170) cc_final: 0.7933 (tpt90) REVERT: N 151 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: H 84 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7982 (mtpt) REVERT: H 108 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8220 (tmtt) REVERT: H 153 MET cc_start: 0.8834 (mmm) cc_final: 0.8379 (tpt) REVERT: I 56 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7584 (mp0) REVERT: I 57 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8343 (mttt) REVERT: I 92 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8564 (ptm) REVERT: I 98 MET cc_start: 0.8137 (tpt) cc_final: 0.7822 (tpt) REVERT: I 144 LYS cc_start: 0.8588 (mttt) cc_final: 0.8333 (mttt) REVERT: I 171 ASP cc_start: 0.8716 (m-30) cc_final: 0.8304 (m-30) REVERT: J 56 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7565 (mp0) REVERT: J 149 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8231 (mmm) REVERT: K 15 ARG cc_start: 0.7763 (ttm170) cc_final: 0.6981 (ttm170) REVERT: K 84 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8009 (mmtm) REVERT: K 118 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7482 (ptt180) REVERT: K 129 GLN cc_start: 0.8365 (tp40) cc_final: 0.8029 (mp10) REVERT: K 144 LYS cc_start: 0.8566 (mttt) cc_final: 0.8352 (mttp) REVERT: K 190 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8331 (m) REVERT: L 118 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7410 (ptp-170) outliers start: 54 outliers final: 16 residues processed: 550 average time/residue: 1.5702 time to fit residues: 966.2487 Evaluate side-chains 477 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 448 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 43 ILE Chi-restraints excluded: chain m residue 94 GLN Chi-restraints excluded: chain m residue 120 MET Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 92 MET Chi-restraints excluded: chain M residue 14 GLU Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 92 MET Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain K residue 190 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 80 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 211 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN l 123 GLN n 41 ASN n 116 ASN n 123 GLN M 34 GLN M 41 ASN H 34 GLN H 163 GLN K 9 GLN L 9 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.091724 restraints weight = 67147.765| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.34 r_work: 0.3007 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21629 Z= 0.149 Angle : 0.500 5.048 29139 Z= 0.263 Chirality : 0.042 0.147 3302 Planarity : 0.004 0.049 3789 Dihedral : 4.157 23.555 2949 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.96 % Allowed : 15.15 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2675 helix: 1.77 (0.15), residues: 1373 sheet: -0.34 (0.31), residues: 263 loop : -0.82 (0.17), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 22 TYR 0.008 0.001 TYR k 77 PHE 0.010 0.001 PHE n 17 HIS 0.006 0.001 HIS m 122 Details of bonding type rmsd covalent geometry : bond 0.00345 (21629) covalent geometry : angle 0.49991 (29139) hydrogen bonds : bond 0.03978 ( 1156) hydrogen bonds : angle 4.07281 ( 3561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 494 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 57 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8213 (mtmt) REVERT: h 92 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8186 (ptt) REVERT: h 129 GLN cc_start: 0.8516 (mt0) cc_final: 0.8309 (mm110) REVERT: i 22 ARG cc_start: 0.8436 (tpt90) cc_final: 0.8118 (tpt90) REVERT: j 22 ARG cc_start: 0.8743 (tpt90) cc_final: 0.8414 (tpt170) REVERT: j 26 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7438 (mt-10) REVERT: j 41 ASN cc_start: 0.8158 (t0) cc_final: 0.7760 (t0) REVERT: j 144 LYS cc_start: 0.8649 (mttt) cc_final: 0.8265 (mttp) REVERT: k 26 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7680 (mm-30) REVERT: k 84 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7666 (ttmt) REVERT: k 108 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8662 (tmtt) REVERT: l 5 MET cc_start: 0.6961 (mpt) cc_final: 0.6750 (mpp) REVERT: l 144 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8141 (mtmt) REVERT: m 25 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7981 (mtpp) REVERT: m 108 LYS cc_start: 0.8778 (tmtt) cc_final: 0.8187 (tppt) REVERT: n 22 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7877 (tpt90) REVERT: n 92 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8275 (ptt) REVERT: n 108 LYS cc_start: 0.8723 (tptm) cc_final: 0.8268 (mmtm) REVERT: M 17 PHE cc_start: 0.7428 (m-80) cc_final: 0.7135 (m-80) REVERT: M 118 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7335 (ptt180) REVERT: N 34 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8300 (tp40) REVERT: N 41 ASN cc_start: 0.7725 (m-40) cc_final: 0.7479 (m110) REVERT: N 57 LYS cc_start: 0.9010 (mtmt) cc_final: 0.8786 (mttt) REVERT: N 148 ARG cc_start: 0.8190 (tpt170) cc_final: 0.7978 (tpt90) REVERT: N 151 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: H 41 ASN cc_start: 0.8269 (m110) cc_final: 0.8058 (m110) REVERT: H 84 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7886 (mtpt) REVERT: H 120 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8644 (ttm) REVERT: H 153 MET cc_start: 0.8818 (mmm) cc_final: 0.8297 (tpt) REVERT: H 186 ASP cc_start: 0.8853 (m-30) cc_final: 0.8598 (m-30) REVERT: I 56 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7684 (mp0) REVERT: I 57 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8427 (mttt) REVERT: I 144 LYS cc_start: 0.8654 (mttt) cc_final: 0.8394 (mttt) REVERT: I 153 MET cc_start: 0.8834 (mmm) cc_final: 0.8542 (tpt) REVERT: I 171 ASP cc_start: 0.8698 (m-30) cc_final: 0.8348 (m-30) REVERT: J 53 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6614 (mm-30) REVERT: J 56 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7772 (mp0) REVERT: J 88 SER cc_start: 0.8881 (t) cc_final: 0.8614 (m) REVERT: J 149 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8300 (mmm) REVERT: K 58 ASP cc_start: 0.7938 (m-30) cc_final: 0.7716 (m-30) REVERT: K 84 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7930 (mmtm) REVERT: K 118 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7608 (ptt180) REVERT: K 129 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: K 144 LYS cc_start: 0.8616 (mttt) cc_final: 0.8399 (mttp) REVERT: K 190 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8321 (m) REVERT: L 92 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8218 (ptp) REVERT: L 118 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7429 (ptt180) outliers start: 45 outliers final: 18 residues processed: 512 average time/residue: 1.4736 time to fit residues: 851.3159 Evaluate side-chains 492 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 463 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain m residue 6 VAL Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 92 MET Chi-restraints excluded: chain n residue 190 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 92 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 20 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 247 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.0020 chunk 111 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN l 41 ASN M 34 GLN M 41 ASN H 34 GLN I 34 GLN I 41 ASN L 9 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.106568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.090927 restraints weight = 67623.146| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.34 r_work: 0.2930 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21629 Z= 0.148 Angle : 0.488 4.867 29139 Z= 0.256 Chirality : 0.041 0.144 3302 Planarity : 0.004 0.045 3789 Dihedral : 4.049 23.311 2949 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.09 % Allowed : 16.24 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.16), residues: 2675 helix: 1.84 (0.15), residues: 1378 sheet: -0.16 (0.32), residues: 232 loop : -0.74 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG m 22 TYR 0.008 0.001 TYR N 62 PHE 0.011 0.001 PHE H 17 HIS 0.006 0.001 HIS m 122 Details of bonding type rmsd covalent geometry : bond 0.00348 (21629) covalent geometry : angle 0.48801 (29139) hydrogen bonds : bond 0.03868 ( 1156) hydrogen bonds : angle 3.96857 ( 3561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 480 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 57 LYS cc_start: 0.8584 (mtpp) cc_final: 0.8191 (mtmt) REVERT: h 92 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8097 (ptt) REVERT: i 22 ARG cc_start: 0.8401 (tpt90) cc_final: 0.8011 (tpt90) REVERT: j 22 ARG cc_start: 0.8681 (tpt90) cc_final: 0.8442 (tpt90) REVERT: j 26 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7328 (mt-10) REVERT: j 41 ASN cc_start: 0.8199 (t0) cc_final: 0.7762 (t0) REVERT: j 144 LYS cc_start: 0.8622 (mttt) cc_final: 0.8076 (mttp) REVERT: k 26 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7564 (mm-30) REVERT: k 84 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7677 (ttmt) REVERT: l 5 MET cc_start: 0.7004 (mpt) cc_final: 0.6781 (mpp) REVERT: l 122 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.8017 (p-80) REVERT: l 144 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8037 (mtmt) REVERT: m 88 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8614 (p) REVERT: m 108 LYS cc_start: 0.8839 (tmtt) cc_final: 0.8244 (tppt) REVERT: n 22 ARG cc_start: 0.8156 (tpt90) cc_final: 0.7942 (tpt90) REVERT: n 92 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8141 (ptm) REVERT: n 108 LYS cc_start: 0.8784 (tptm) cc_final: 0.8180 (mmtm) REVERT: M 118 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7252 (ptt180) REVERT: N 34 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8295 (tp40) REVERT: N 41 ASN cc_start: 0.7768 (m-40) cc_final: 0.7480 (m110) REVERT: N 57 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8748 (mttt) REVERT: N 148 ARG cc_start: 0.8168 (tpt170) cc_final: 0.7958 (tpt90) REVERT: N 151 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: H 84 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7814 (mtpt) REVERT: H 108 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8180 (tmtt) REVERT: H 120 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8649 (ttm) REVERT: H 153 MET cc_start: 0.8792 (mmm) cc_final: 0.8263 (tpt) REVERT: I 56 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7687 (mp0) REVERT: I 57 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8428 (mttt) REVERT: I 144 LYS cc_start: 0.8599 (mttt) cc_final: 0.8327 (mttt) REVERT: I 153 MET cc_start: 0.8787 (mmm) cc_final: 0.8562 (tpt) REVERT: I 171 ASP cc_start: 0.8704 (m-30) cc_final: 0.8347 (m-30) REVERT: J 53 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6722 (mm-30) REVERT: J 56 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7768 (mp0) REVERT: J 88 SER cc_start: 0.8870 (t) cc_final: 0.8661 (m) REVERT: J 149 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8242 (mmm) REVERT: K 84 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7722 (mmtm) REVERT: K 118 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7565 (ptt180) REVERT: K 144 LYS cc_start: 0.8585 (mttt) cc_final: 0.8364 (mttp) REVERT: K 190 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8319 (m) REVERT: L 92 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8361 (ptp) REVERT: L 118 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7370 (ptt180) outliers start: 48 outliers final: 22 residues processed: 494 average time/residue: 1.4928 time to fit residues: 833.6438 Evaluate side-chains 493 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 460 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 122 HIS Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 120 MET Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 92 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain K residue 39 MET Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 92 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 129 GLN i 41 ASN k 41 ASN l 41 ASN M 34 GLN M 41 ASN N 41 ASN H 34 GLN L 9 GLN L 129 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.103318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.087748 restraints weight = 67932.413| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.34 r_work: 0.2888 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21629 Z= 0.205 Angle : 0.524 5.029 29139 Z= 0.279 Chirality : 0.043 0.145 3302 Planarity : 0.004 0.034 3789 Dihedral : 4.192 23.422 2949 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.44 % Allowed : 16.46 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2675 helix: 1.80 (0.15), residues: 1363 sheet: -0.11 (0.32), residues: 235 loop : -0.88 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 192 TYR 0.013 0.001 TYR N 62 PHE 0.013 0.001 PHE H 17 HIS 0.006 0.002 HIS m 122 Details of bonding type rmsd covalent geometry : bond 0.00488 (21629) covalent geometry : angle 0.52432 (29139) hydrogen bonds : bond 0.04412 ( 1156) hydrogen bonds : angle 4.08606 ( 3561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 477 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 5 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6685 (mmt) REVERT: h 57 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8288 (mtmt) REVERT: h 92 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8231 (ptt) REVERT: i 22 ARG cc_start: 0.8423 (tpt90) cc_final: 0.8011 (tpt90) REVERT: j 22 ARG cc_start: 0.8730 (tpt90) cc_final: 0.8451 (tpt90) REVERT: j 26 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7389 (mt-10) REVERT: j 41 ASN cc_start: 0.8245 (t0) cc_final: 0.7833 (t0) REVERT: j 144 LYS cc_start: 0.8645 (mttt) cc_final: 0.8093 (mttp) REVERT: k 26 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7613 (mm-30) REVERT: k 84 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7806 (ttmt) REVERT: k 108 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8683 (tmtt) REVERT: l 5 MET cc_start: 0.6978 (mpt) cc_final: 0.6747 (mpp) REVERT: l 144 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8099 (mtmt) REVERT: m 84 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7280 (mttp) REVERT: m 88 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8726 (t) REVERT: m 108 LYS cc_start: 0.8895 (tmtt) cc_final: 0.8274 (tppt) REVERT: m 118 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7034 (ptp-170) REVERT: n 92 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8215 (ptm) REVERT: n 108 LYS cc_start: 0.8845 (tptm) cc_final: 0.8156 (mmtm) REVERT: M 118 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7239 (ptt180) REVERT: N 34 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8337 (tp40) REVERT: N 57 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8778 (mttt) REVERT: N 148 ARG cc_start: 0.8160 (tpt170) cc_final: 0.7954 (tpt90) REVERT: N 151 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: H 84 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7932 (mtpt) REVERT: H 92 MET cc_start: 0.8889 (ptp) cc_final: 0.8581 (ptt) REVERT: H 108 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8206 (tmtt) REVERT: H 120 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8684 (ttm) REVERT: H 153 MET cc_start: 0.8798 (mmm) cc_final: 0.8426 (tpt) REVERT: I 56 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7767 (mp0) REVERT: I 57 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8459 (mttt) REVERT: I 144 LYS cc_start: 0.8616 (mttt) cc_final: 0.8352 (mttt) REVERT: I 153 MET cc_start: 0.8795 (mmm) cc_final: 0.8442 (tpt) REVERT: I 171 ASP cc_start: 0.8745 (m-30) cc_final: 0.8368 (m-30) REVERT: J 56 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7843 (mp0) REVERT: K 15 ARG cc_start: 0.7795 (ttm170) cc_final: 0.7496 (ttp-170) REVERT: K 84 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7723 (mmtm) REVERT: K 118 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7553 (ptt180) REVERT: K 129 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: K 144 LYS cc_start: 0.8601 (mttt) cc_final: 0.8351 (mttt) REVERT: K 190 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8424 (m) REVERT: L 15 ARG cc_start: 0.8180 (ptp-170) cc_final: 0.7976 (ptp-170) REVERT: L 34 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8168 (tp40) REVERT: L 58 ASP cc_start: 0.7970 (m-30) cc_final: 0.7709 (m-30) REVERT: L 92 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8380 (ptp) REVERT: L 118 ARG cc_start: 0.8172 (mtt-85) cc_final: 0.7358 (ptt180) outliers start: 56 outliers final: 27 residues processed: 496 average time/residue: 1.4720 time to fit residues: 823.9936 Evaluate side-chains 492 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 454 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 6 VAL Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 6 VAL Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 120 MET Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 92 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 92 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 228 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN l 41 ASN M 34 GLN M 41 ASN H 34 GLN H 41 ASN I 34 GLN L 9 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.101603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.086122 restraints weight = 68222.748| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.33 r_work: 0.2864 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21629 Z= 0.247 Angle : 0.552 5.395 29139 Z= 0.296 Chirality : 0.044 0.146 3302 Planarity : 0.004 0.056 3789 Dihedral : 4.380 23.531 2949 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.53 % Allowed : 16.63 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.16), residues: 2675 helix: 1.62 (0.15), residues: 1367 sheet: -0.02 (0.31), residues: 239 loop : -0.95 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG m 22 TYR 0.017 0.002 TYR k 62 PHE 0.016 0.001 PHE H 17 HIS 0.007 0.002 HIS N 38 Details of bonding type rmsd covalent geometry : bond 0.00591 (21629) covalent geometry : angle 0.55182 (29139) hydrogen bonds : bond 0.04805 ( 1156) hydrogen bonds : angle 4.21841 ( 3561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 466 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 2 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.5929 (mt) REVERT: h 5 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6893 (mmt) REVERT: h 57 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8308 (mtmt) REVERT: h 92 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8287 (ptt) REVERT: h 129 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: i 22 ARG cc_start: 0.8476 (tpt90) cc_final: 0.8155 (tpt90) REVERT: j 22 ARG cc_start: 0.8749 (tpt90) cc_final: 0.8501 (tpt90) REVERT: j 26 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7512 (mt-10) REVERT: j 41 ASN cc_start: 0.8277 (t0) cc_final: 0.7888 (t0) REVERT: j 144 LYS cc_start: 0.8655 (mttt) cc_final: 0.8084 (mttp) REVERT: k 26 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7631 (mm-30) REVERT: k 47 MET cc_start: 0.8992 (mtt) cc_final: 0.8666 (mtt) REVERT: k 84 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8038 (ttmt) REVERT: k 108 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8700 (tmtt) REVERT: k 140 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7790 (mtm110) REVERT: l 5 MET cc_start: 0.7007 (mpt) cc_final: 0.6789 (mpp) REVERT: m 84 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7809 (mtpt) REVERT: m 108 LYS cc_start: 0.8874 (tmtt) cc_final: 0.8209 (tppt) REVERT: n 92 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8193 (ptt) REVERT: n 108 LYS cc_start: 0.8908 (tptm) cc_final: 0.8120 (mmtm) REVERT: n 171 ASP cc_start: 0.8264 (m-30) cc_final: 0.7901 (m-30) REVERT: M 92 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8439 (ptp) REVERT: M 118 ARG cc_start: 0.8012 (mtt-85) cc_final: 0.7282 (ptt180) REVERT: N 34 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8341 (tp40) REVERT: N 57 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8775 (mttt) REVERT: N 148 ARG cc_start: 0.8129 (tpt170) cc_final: 0.7921 (tpt90) REVERT: N 151 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: H 92 MET cc_start: 0.8963 (ptp) cc_final: 0.8611 (ptt) REVERT: H 108 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8216 (tmtt) REVERT: H 153 MET cc_start: 0.8836 (mmm) cc_final: 0.8457 (tpt) REVERT: I 56 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7785 (mp0) REVERT: I 57 LYS cc_start: 0.8786 (mtpp) cc_final: 0.8456 (mttt) REVERT: I 92 MET cc_start: 0.9193 (ptp) cc_final: 0.8808 (ptt) REVERT: I 144 LYS cc_start: 0.8604 (mttt) cc_final: 0.8344 (mttt) REVERT: I 153 MET cc_start: 0.8828 (mmm) cc_final: 0.8448 (tpt) REVERT: I 171 ASP cc_start: 0.8742 (m-30) cc_final: 0.8369 (m-30) REVERT: J 56 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7814 (mp0) REVERT: J 149 MET cc_start: 0.8777 (mmm) cc_final: 0.8550 (mmm) REVERT: K 15 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7222 (tpt170) REVERT: K 84 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7699 (mmtm) REVERT: K 118 ARG cc_start: 0.8268 (mtt-85) cc_final: 0.7484 (ptt180) REVERT: K 129 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: K 190 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8451 (m) REVERT: L 5 MET cc_start: 0.8710 (mmm) cc_final: 0.8475 (mmm) REVERT: L 9 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8178 (mm110) REVERT: L 34 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8273 (tp40) REVERT: L 92 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8417 (ptp) REVERT: L 118 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7367 (ptt180) outliers start: 58 outliers final: 31 residues processed: 491 average time/residue: 1.4913 time to fit residues: 825.0211 Evaluate side-chains 487 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 444 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain h residue 2 LEU Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain h residue 129 GLN Chi-restraints excluded: chain j residue 6 VAL Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 6 VAL Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 120 MET Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 92 MET Chi-restraints excluded: chain n residue 190 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 92 MET Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 92 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 188 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN k 129 GLN l 41 ASN M 41 ASN N 129 GLN H 41 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.104211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.088775 restraints weight = 67739.121| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.32 r_work: 0.2903 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21629 Z= 0.142 Angle : 0.492 5.399 29139 Z= 0.259 Chirality : 0.041 0.145 3302 Planarity : 0.004 0.067 3789 Dihedral : 4.235 23.960 2949 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.92 % Allowed : 17.33 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2675 helix: 1.76 (0.15), residues: 1371 sheet: -0.13 (0.30), residues: 289 loop : -0.83 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 22 TYR 0.008 0.001 TYR m 60 PHE 0.011 0.001 PHE H 17 HIS 0.005 0.001 HIS h 122 Details of bonding type rmsd covalent geometry : bond 0.00334 (21629) covalent geometry : angle 0.49165 (29139) hydrogen bonds : bond 0.03821 ( 1156) hydrogen bonds : angle 3.98382 ( 3561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 469 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 2 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.5885 (mt) REVERT: h 5 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6907 (mmt) REVERT: h 57 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8306 (mtmt) REVERT: i 22 ARG cc_start: 0.8444 (tpt90) cc_final: 0.7966 (tpt90) REVERT: j 22 ARG cc_start: 0.8668 (tpt90) cc_final: 0.8459 (tpt170) REVERT: j 26 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7545 (mt-10) REVERT: j 41 ASN cc_start: 0.8214 (t0) cc_final: 0.7812 (t0) REVERT: j 144 LYS cc_start: 0.8637 (mttt) cc_final: 0.8080 (mttp) REVERT: k 26 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7639 (mm-30) REVERT: k 47 MET cc_start: 0.8929 (mtt) cc_final: 0.8626 (mtt) REVERT: k 84 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7878 (ttmt) REVERT: l 5 MET cc_start: 0.6922 (mpt) cc_final: 0.6696 (mpp) REVERT: l 144 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8098 (mtmt) REVERT: m 108 LYS cc_start: 0.8875 (tmtt) cc_final: 0.8177 (tppt) REVERT: n 108 LYS cc_start: 0.8862 (tptm) cc_final: 0.8070 (mmtm) REVERT: M 118 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7240 (ptt180) REVERT: N 26 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7449 (mt-10) REVERT: N 34 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8349 (tp40) REVERT: N 57 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8714 (mttt) REVERT: N 148 ARG cc_start: 0.8109 (tpt170) cc_final: 0.7898 (tpt90) REVERT: N 151 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: H 108 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8124 (tmtt) REVERT: H 153 MET cc_start: 0.8808 (mmm) cc_final: 0.8285 (tpt) REVERT: H 186 ASP cc_start: 0.8902 (m-30) cc_final: 0.8631 (m-30) REVERT: I 56 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7813 (mp0) REVERT: I 57 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8440 (mttt) REVERT: I 92 MET cc_start: 0.9092 (ptp) cc_final: 0.8672 (ptt) REVERT: I 144 LYS cc_start: 0.8568 (mttt) cc_final: 0.8317 (mttt) REVERT: I 153 MET cc_start: 0.8807 (mmm) cc_final: 0.8513 (tpt) REVERT: I 171 ASP cc_start: 0.8733 (m-30) cc_final: 0.8379 (m-30) REVERT: J 56 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7811 (mp0) REVERT: J 149 MET cc_start: 0.8754 (mmm) cc_final: 0.8522 (mmm) REVERT: K 15 ARG cc_start: 0.7782 (ttm170) cc_final: 0.7204 (ttt180) REVERT: K 84 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7685 (mmtm) REVERT: K 118 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.7514 (ptt180) REVERT: K 129 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: K 190 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8389 (m) REVERT: L 5 MET cc_start: 0.8699 (mmm) cc_final: 0.8493 (mmm) REVERT: L 34 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8214 (tp40) REVERT: L 92 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8396 (ptp) REVERT: L 118 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7425 (ptt180) outliers start: 44 outliers final: 28 residues processed: 484 average time/residue: 1.4905 time to fit residues: 813.5158 Evaluate side-chains 492 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 457 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 2 LEU Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 6 VAL Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 120 MET Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 92 MET Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 92 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 242 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN l 41 ASN M 41 ASN N 129 GLN H 41 ASN L 9 GLN L 129 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.086606 restraints weight = 68040.312| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.33 r_work: 0.2873 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21629 Z= 0.215 Angle : 0.528 5.116 29139 Z= 0.282 Chirality : 0.043 0.144 3302 Planarity : 0.004 0.058 3789 Dihedral : 4.333 25.834 2949 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.96 % Allowed : 17.98 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 2675 helix: 1.72 (0.15), residues: 1362 sheet: -0.05 (0.27), residues: 347 loop : -0.89 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG l 22 TYR 0.013 0.002 TYR k 62 PHE 0.014 0.001 PHE m 17 HIS 0.005 0.002 HIS h 122 Details of bonding type rmsd covalent geometry : bond 0.00515 (21629) covalent geometry : angle 0.52827 (29139) hydrogen bonds : bond 0.04469 ( 1156) hydrogen bonds : angle 4.13884 ( 3561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 458 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 2 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.5907 (mt) REVERT: h 5 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6940 (mmt) REVERT: h 57 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8398 (mtmt) REVERT: h 129 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: i 22 ARG cc_start: 0.8488 (tpt90) cc_final: 0.7992 (tpt90) REVERT: j 26 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7588 (mt-10) REVERT: j 41 ASN cc_start: 0.8265 (t0) cc_final: 0.7869 (t0) REVERT: j 144 LYS cc_start: 0.8660 (mttt) cc_final: 0.8097 (mttp) REVERT: k 26 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7644 (mm-30) REVERT: k 84 LYS cc_start: 0.8318 (ttpp) cc_final: 0.8006 (ttmt) REVERT: k 108 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8654 (tmtt) REVERT: k 140 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7806 (mtm110) REVERT: l 5 MET cc_start: 0.6986 (mpt) cc_final: 0.6754 (mpp) REVERT: l 144 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8144 (mtmt) REVERT: m 108 LYS cc_start: 0.8859 (tmtt) cc_final: 0.8176 (tppt) REVERT: n 22 ARG cc_start: 0.8406 (tpt90) cc_final: 0.8195 (tpt90) REVERT: n 108 LYS cc_start: 0.8882 (tptm) cc_final: 0.8048 (mmtm) REVERT: n 171 ASP cc_start: 0.8257 (m-30) cc_final: 0.7899 (m-30) REVERT: M 118 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.7262 (ptt180) REVERT: N 34 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8333 (tp40) REVERT: N 57 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8753 (mttt) REVERT: N 148 ARG cc_start: 0.8165 (tpt170) cc_final: 0.7945 (tpt90) REVERT: N 151 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: H 108 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8201 (tmtt) REVERT: H 120 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8730 (ttm) REVERT: H 153 MET cc_start: 0.8840 (mmm) cc_final: 0.8321 (tpt) REVERT: I 56 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7770 (mp0) REVERT: I 57 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8450 (mttt) REVERT: I 144 LYS cc_start: 0.8585 (mttt) cc_final: 0.8326 (mttt) REVERT: I 153 MET cc_start: 0.8838 (mmm) cc_final: 0.8443 (tpt) REVERT: I 171 ASP cc_start: 0.8723 (m-30) cc_final: 0.8336 (m-30) REVERT: J 56 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7831 (mp0) REVERT: J 149 MET cc_start: 0.8771 (mmm) cc_final: 0.8545 (mmm) REVERT: K 15 ARG cc_start: 0.7774 (ttm170) cc_final: 0.7126 (tpt170) REVERT: K 84 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7699 (mmtm) REVERT: K 118 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.7501 (ptt180) REVERT: K 129 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: L 5 MET cc_start: 0.8691 (mmm) cc_final: 0.8483 (mmm) REVERT: L 34 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8253 (tp40) REVERT: L 92 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8406 (ptp) REVERT: L 118 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7425 (ptt180) outliers start: 45 outliers final: 28 residues processed: 474 average time/residue: 1.5276 time to fit residues: 815.3981 Evaluate side-chains 489 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 451 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 2 LEU Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain h residue 129 GLN Chi-restraints excluded: chain j residue 6 VAL Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 36 GLU Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 6 VAL Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 120 MET Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 92 MET Chi-restraints excluded: chain L residue 118 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 92 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 251 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 163 GLN i 41 ASN k 41 ASN l 41 ASN M 41 ASN H 41 ASN I 9 GLN K 9 GLN L 9 GLN L 129 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.105075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.089667 restraints weight = 67671.757| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.32 r_work: 0.2917 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21629 Z= 0.125 Angle : 0.480 7.121 29139 Z= 0.251 Chirality : 0.041 0.143 3302 Planarity : 0.004 0.045 3789 Dihedral : 4.185 24.622 2949 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.52 % Allowed : 18.46 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2675 helix: 1.85 (0.15), residues: 1371 sheet: -0.03 (0.27), residues: 349 loop : -0.83 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 22 TYR 0.007 0.001 TYR n 77 PHE 0.012 0.001 PHE m 17 HIS 0.005 0.001 HIS h 122 Details of bonding type rmsd covalent geometry : bond 0.00295 (21629) covalent geometry : angle 0.47959 (29139) hydrogen bonds : bond 0.03555 ( 1156) hydrogen bonds : angle 3.91273 ( 3561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 469 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 2 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5862 (mt) REVERT: h 5 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6886 (mmt) REVERT: h 57 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8395 (mtmt) REVERT: h 129 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: i 22 ARG cc_start: 0.8451 (tpt90) cc_final: 0.8198 (tpt90) REVERT: j 41 ASN cc_start: 0.8197 (t0) cc_final: 0.7786 (t0) REVERT: j 144 LYS cc_start: 0.8642 (mttt) cc_final: 0.8084 (mttp) REVERT: k 26 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7648 (mm-30) REVERT: k 47 MET cc_start: 0.8919 (mtt) cc_final: 0.8612 (mtt) REVERT: k 84 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7872 (ttmt) REVERT: k 108 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8634 (tmtt) REVERT: l 5 MET cc_start: 0.6919 (mpt) cc_final: 0.6716 (mpp) REVERT: l 144 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8109 (mtmt) REVERT: m 108 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8149 (tppt) REVERT: n 108 LYS cc_start: 0.8860 (tptm) cc_final: 0.8022 (mmtm) REVERT: N 34 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8291 (tp40) REVERT: N 57 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8709 (mttt) REVERT: N 148 ARG cc_start: 0.8118 (tpt170) cc_final: 0.7904 (tpt90) REVERT: N 151 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: H 108 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8157 (tmtt) REVERT: H 120 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8720 (ttm) REVERT: H 153 MET cc_start: 0.8805 (mmm) cc_final: 0.8276 (tpt) REVERT: H 186 ASP cc_start: 0.8886 (m-30) cc_final: 0.8625 (m-30) REVERT: I 56 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7768 (mp0) REVERT: I 57 LYS cc_start: 0.8787 (mtpp) cc_final: 0.8474 (mttt) REVERT: I 144 LYS cc_start: 0.8515 (mttt) cc_final: 0.8259 (mttt) REVERT: I 153 MET cc_start: 0.8801 (mmm) cc_final: 0.8504 (tpt) REVERT: I 171 ASP cc_start: 0.8715 (m-30) cc_final: 0.8342 (m-30) REVERT: J 56 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7829 (mp0) REVERT: J 149 MET cc_start: 0.8761 (mmm) cc_final: 0.8508 (mmm) REVERT: K 15 ARG cc_start: 0.7786 (ttm170) cc_final: 0.7180 (ttt180) REVERT: K 84 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7665 (mmtm) REVERT: K 118 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7525 (ptt180) REVERT: K 129 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: L 34 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8181 (tp40) REVERT: L 92 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8333 (ptp) REVERT: L 118 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7416 (ptt180) outliers start: 35 outliers final: 19 residues processed: 479 average time/residue: 1.4445 time to fit residues: 781.2109 Evaluate side-chains 484 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 455 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 2 LEU Chi-restraints excluded: chain h residue 5 MET Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain h residue 129 GLN Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 120 MET Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 92 MET Chi-restraints excluded: chain L residue 118 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 151 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN l 41 ASN M 41 ASN H 41 ASN L 9 GLN L 129 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.102602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.087133 restraints weight = 68288.872| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.33 r_work: 0.2879 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21629 Z= 0.203 Angle : 0.519 4.992 29139 Z= 0.277 Chirality : 0.042 0.143 3302 Planarity : 0.004 0.050 3789 Dihedral : 4.292 26.389 2949 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.65 % Allowed : 18.37 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2675 helix: 1.81 (0.15), residues: 1362 sheet: 0.01 (0.27), residues: 349 loop : -0.90 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 22 TYR 0.012 0.001 TYR k 62 PHE 0.011 0.001 PHE H 17 HIS 0.005 0.002 HIS h 122 Details of bonding type rmsd covalent geometry : bond 0.00483 (21629) covalent geometry : angle 0.51913 (29139) hydrogen bonds : bond 0.04275 ( 1156) hydrogen bonds : angle 4.07540 ( 3561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15539.20 seconds wall clock time: 262 minutes 51.19 seconds (15771.19 seconds total)