Starting phenix.real_space_refine on Wed Feb 21 14:26:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1m_0592/02_2024/6o1m_0592.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1m_0592/02_2024/6o1m_0592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1m_0592/02_2024/6o1m_0592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1m_0592/02_2024/6o1m_0592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1m_0592/02_2024/6o1m_0592.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1m_0592/02_2024/6o1m_0592.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 34 5.49 5 S 48 5.16 5 C 9894 2.51 5 N 2777 2.21 5 O 2923 1.98 5 H 15371 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 230": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 239": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 230": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 239": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 18": "OE1" <-> "OE2" Residue "D ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31047 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "B" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "C" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "D" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "E" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "F" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "G" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1100 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "H" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "I" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "J" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "K" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "L" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1095 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain: "M" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "N" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1100 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "O" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Classifications: {'RNA': 18} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 15, 'rna2p_pyr': 3} Link IDs: {'rna2p': 17} Chain: "P" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Classifications: {'RNA': 18} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 15, 'rna2p_pyr': 3} Link IDs: {'rna2p': 17} Chain: "R" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "S" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Time building chain proxies: 13.25, per 1000 atoms: 0.43 Number of scatterers: 31047 At special positions: 0 Unit cell: (101.37, 122.08, 107.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 34 15.00 O 2923 8.00 N 2777 7.00 C 9894 6.00 H 15371 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.04 Conformation dependent library (CDL) restraints added in 3.1 seconds 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3490 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 25.3% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.50 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.616A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.522A pdb=" N TRP A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.553A pdb=" N ARG A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.553A pdb=" N VAL A 158 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.500A pdb=" N GLU A 163 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.993A pdb=" N VAL A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.765A pdb=" N LEU A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.598A pdb=" N ARG A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 39 through 44 removed outlier: 3.829A pdb=" N ASP B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 115 through 136 removed outlier: 3.791A pdb=" N LYS B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 171 through 182 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 226 through 229 removed outlier: 3.756A pdb=" N ARG B 229 " --> pdb=" O PRO B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'C' and resid 7 through 18 Processing helix chain 'D' and resid 7 through 18 removed outlier: 3.768A pdb=" N TYR D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 18 removed outlier: 3.635A pdb=" N TYR E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 18 Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.232A pdb=" N TYR G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 18 Processing helix chain 'I' and resid 7 through 18 removed outlier: 3.596A pdb=" N GLU I 18 " --> pdb=" O THR I 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 18 removed outlier: 3.632A pdb=" N TYR J 11 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU J 18 " --> pdb=" O THR J 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 19 removed outlier: 3.771A pdb=" N TYR K 11 " --> pdb=" O LEU K 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 18 removed outlier: 3.569A pdb=" N TYR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 18 removed outlier: 3.829A pdb=" N TYR M 11 " --> pdb=" O LEU M 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 18 removed outlier: 3.980A pdb=" N TYR N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG N 16 " --> pdb=" O LEU N 12 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU N 18 " --> pdb=" O THR N 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 16 removed outlier: 3.755A pdb=" N GLU R 16 " --> pdb=" O GLN R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 24 Processing helix chain 'R' and resid 25 through 27 No H-bonds generated for 'chain 'R' and resid 25 through 27' Processing helix chain 'R' and resid 85 through 90 removed outlier: 3.682A pdb=" N ASP R 89 " --> pdb=" O PHE R 85 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG R 90 " --> pdb=" O GLU R 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 85 through 90' Processing helix chain 'R' and resid 115 through 137 removed outlier: 3.590A pdb=" N LEU R 119 " --> pdb=" O GLY R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 164 removed outlier: 3.842A pdb=" N GLU R 163 " --> pdb=" O ASN R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 182 removed outlier: 3.540A pdb=" N LEU R 178 " --> pdb=" O GLU R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 195 removed outlier: 4.210A pdb=" N VAL R 194 " --> pdb=" O ALA R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 213 Processing helix chain 'R' and resid 228 through 230 No H-bonds generated for 'chain 'R' and resid 228 through 230' Processing helix chain 'S' and resid 10 through 16 Processing helix chain 'S' and resid 18 through 25 removed outlier: 3.954A pdb=" N ALA S 25 " --> pdb=" O SER S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 removed outlier: 3.593A pdb=" N ASP S 45 " --> pdb=" O ASP S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 66 removed outlier: 3.625A pdb=" N GLY S 66 " --> pdb=" O PRO S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 90 removed outlier: 3.674A pdb=" N ASP S 89 " --> pdb=" O PHE S 85 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG S 90 " --> pdb=" O GLU S 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 85 through 90' Processing helix chain 'S' and resid 115 through 137 Processing helix chain 'S' and resid 154 through 158 removed outlier: 4.029A pdb=" N VAL S 158 " --> pdb=" O LYS S 155 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 164 removed outlier: 3.906A pdb=" N GLU S 163 " --> pdb=" O ASN S 160 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS S 164 " --> pdb=" O TRP S 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 160 through 164' Processing helix chain 'S' and resid 171 through 182 removed outlier: 3.697A pdb=" N LEU S 178 " --> pdb=" O GLU S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 removed outlier: 6.719A pdb=" N ARG A 2 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N CYS A 32 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 4 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN A 34 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 7.040A pdb=" N SER A 103 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N CYS A 146 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA A 105 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N SER A 148 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A 107 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 58 removed outlier: 6.688A pdb=" N ARG B 2 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS B 32 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 4 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLN B 34 " --> pdb=" O ILE B 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 81 removed outlier: 6.843A pdb=" N SER B 103 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N CYS B 146 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B 105 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER B 148 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU B 107 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.932A pdb=" N SER D 38 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS D 47 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE D 36 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 34 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 61 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 43 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE C 39 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU C 45 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER C 23 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL C 62 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR C 25 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C 60 " --> pdb=" O TYR G 55 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL G 43 " --> pdb=" O PHE G 39 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE G 39 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU G 45 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER G 60 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET H 53 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER H 51 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER H 38 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS H 47 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE H 36 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER H 60 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE F 39 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU F 45 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER F 60 " --> pdb=" O TYR E 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.545A pdb=" N SER E 23 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL E 62 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR E 25 " --> pdb=" O SER E 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 22 through 26 removed outlier: 6.777A pdb=" N LEU I 45 " --> pdb=" O GLU I 37 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE I 39 " --> pdb=" O VAL I 43 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL I 43 " --> pdb=" O PHE I 39 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N SER I 51 " --> pdb=" O PRO J 64 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER J 60 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU J 45 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE J 39 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL J 43 " --> pdb=" O PHE J 39 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER J 51 " --> pdb=" O PRO K 64 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER K 60 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU K 45 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE K 39 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL K 43 " --> pdb=" O PHE K 39 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER K 51 " --> pdb=" O PRO L 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET K 53 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER L 60 " --> pdb=" O TYR K 55 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE L 36 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS L 47 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET L 53 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER M 60 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU M 45 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE M 39 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL M 43 " --> pdb=" O PHE M 39 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER N 60 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU N 45 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE N 39 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL N 43 " --> pdb=" O PHE N 39 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER I 60 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR I 25 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL I 62 " --> pdb=" O SER I 23 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER I 23 " --> pdb=" O VAL I 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 54 through 58 removed outlier: 6.555A pdb=" N ARG R 2 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N CYS R 32 " --> pdb=" O ARG R 2 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE R 4 " --> pdb=" O CYS R 32 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLN R 34 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL R 6 " --> pdb=" O GLN R 34 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 78 through 81 Processing sheet with id=AB1, first strand: chain 'S' and resid 54 through 58 removed outlier: 6.542A pdb=" N ARG S 2 " --> pdb=" O VAL S 30 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N CYS S 32 " --> pdb=" O ARG S 2 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE S 4 " --> pdb=" O CYS S 32 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLN S 34 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL S 6 " --> pdb=" O GLN S 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 78 through 81 removed outlier: 3.560A pdb=" N SER S 148 " --> pdb=" O LEU S 107 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1545 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: 12.38 Time building geometry restraints manager: 25.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 3622 1.04 - 1.23: 12089 1.23 - 1.42: 6605 1.42 - 1.62: 9090 1.62 - 1.81: 80 Bond restraints: 31486 Sorted by residual: bond pdb=" ND2 ASN H 28 " pdb="HD22 ASN H 28 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE2 TYR I 55 " pdb=" HE2 TYR I 55 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD1 PHE S 219 " pdb=" HD1 PHE S 219 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL H 43 " pdb=" H VAL H 43 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ASP A 220 " pdb=" H ASP A 220 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 31481 not shown) Histogram of bond angle deviations from ideal: 91.02 - 101.89: 66 101.89 - 112.76: 36107 112.76 - 123.64: 19501 123.64 - 134.51: 1181 134.51 - 145.38: 1 Bond angle restraints: 56856 Sorted by residual: angle pdb=" C6 A O 2 " pdb=" N6 A O 2 " pdb=" H62 A O 2 " ideal model delta sigma weight residual 120.00 91.02 28.98 3.00e+00 1.11e-01 9.33e+01 angle pdb=" C6 A O 2 " pdb=" N6 A O 2 " pdb=" H61 A O 2 " ideal model delta sigma weight residual 120.00 145.38 -25.38 3.00e+00 1.11e-01 7.16e+01 angle pdb=" OE1 GLN G 52 " pdb=" CD GLN G 52 " pdb=" NE2 GLN G 52 " ideal model delta sigma weight residual 122.60 116.60 6.00 1.00e+00 1.00e+00 3.60e+01 angle pdb=" C GLN C 41 " pdb=" N PHE C 42 " pdb=" CA PHE C 42 " ideal model delta sigma weight residual 122.08 130.27 -8.19 1.47e+00 4.63e-01 3.10e+01 angle pdb=" C6 A P 4 " pdb=" N6 A P 4 " pdb=" H61 A P 4 " ideal model delta sigma weight residual 120.00 103.42 16.58 3.00e+00 1.11e-01 3.05e+01 ... (remaining 56851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13397 17.97 - 35.93: 679 35.93 - 53.90: 298 53.90 - 71.87: 318 71.87 - 89.83: 52 Dihedral angle restraints: 14744 sinusoidal: 8342 harmonic: 6402 Sorted by residual: dihedral pdb=" CA ASP H 9 " pdb=" C ASP H 9 " pdb=" N PRO H 10 " pdb=" CA PRO H 10 " ideal model delta harmonic sigma weight residual 180.00 139.08 40.92 0 5.00e+00 4.00e-02 6.70e+01 dihedral pdb=" CA LYS M 47 " pdb=" C LYS M 47 " pdb=" N ASN M 48 " pdb=" CA ASN M 48 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU A 62 " pdb=" C LEU A 62 " pdb=" N PRO A 63 " pdb=" CA PRO A 63 " ideal model delta harmonic sigma weight residual -180.00 -155.07 -24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 14741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1924 0.070 - 0.140: 436 0.140 - 0.211: 67 0.211 - 0.281: 15 0.281 - 0.351: 3 Chirality restraints: 2445 Sorted by residual: chirality pdb=" CB VAL C 43 " pdb=" CA VAL C 43 " pdb=" CG1 VAL C 43 " pdb=" CG2 VAL C 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB ILE N 24 " pdb=" CA ILE N 24 " pdb=" CG1 ILE N 24 " pdb=" CG2 ILE N 24 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE D 24 " pdb=" CA ILE D 24 " pdb=" CG1 ILE D 24 " pdb=" CG2 ILE D 24 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2442 not shown) Planarity restraints: 4465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN S 240 " -0.215 2.00e-02 2.50e+03 4.06e-01 2.48e+03 pdb=" CD GLN S 240 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN S 240 " 0.205 2.00e-02 2.50e+03 pdb=" NE2 GLN S 240 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN S 240 " 0.662 2.00e-02 2.50e+03 pdb="HE22 GLN S 240 " -0.681 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN R 240 " -0.224 2.00e-02 2.50e+03 2.56e-01 9.80e+02 pdb=" CD GLN R 240 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN R 240 " 0.209 2.00e-02 2.50e+03 pdb=" NE2 GLN R 240 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN R 240 " 0.379 2.00e-02 2.50e+03 pdb="HE22 GLN R 240 " -0.392 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 A P 10 " -0.066 2.00e-02 2.50e+03 1.51e-01 2.29e+02 pdb=" N6 A P 10 " 0.261 2.00e-02 2.50e+03 pdb=" H61 A P 10 " -0.095 2.00e-02 2.50e+03 pdb=" H62 A P 10 " -0.100 2.00e-02 2.50e+03 ... (remaining 4462 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.81: 360 1.81 - 2.51: 21717 2.51 - 3.20: 93512 3.20 - 3.90: 128795 3.90 - 4.60: 196130 Nonbonded interactions: 440514 Sorted by model distance: nonbonded pdb=" HG SER K 38 " pdb=" H PHE K 39 " model vdw 1.108 2.100 nonbonded pdb=" HG SER I 38 " pdb=" H PHE I 39 " model vdw 1.179 2.100 nonbonded pdb=" HG SER N 60 " pdb=" H THR N 61 " model vdw 1.261 2.100 nonbonded pdb=" HG SER F 60 " pdb=" H THR F 61 " model vdw 1.294 2.100 nonbonded pdb=" H1 HIS N 5 " pdb=" H SER N 6 " model vdw 1.302 2.100 ... (remaining 440509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'R' selection = chain 'S' } ncs_group { reference = (chain 'C' and resid 6 through 69) selection = (chain 'D' and resid 6 through 69) selection = (chain 'E' and resid 6 through 69) selection = (chain 'F' and resid 6 through 69) selection = (chain 'G' and resid 6 through 69) selection = (chain 'H' and resid 6 through 69) selection = (chain 'I' and resid 6 through 69) selection = (chain 'J' and resid 6 through 69) selection = (chain 'K' and resid 6 through 69) selection = (chain 'L' and resid 6 through 69) selection = (chain 'M' and resid 6 through 69) selection = (chain 'N' and resid 6 through 69) } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.410 Extract box with map and model: 3.370 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 109.120 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.006 0.069 16115 Z= 0.368 Angle : 0.993 13.362 22023 Z= 0.556 Chirality : 0.062 0.351 2445 Planarity : 0.008 0.111 2708 Dihedral : 12.658 89.831 6205 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.55 % Allowed : 5.55 % Favored : 93.91 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.17), residues: 1809 helix: -2.95 (0.19), residues: 345 sheet: -2.23 (0.19), residues: 582 loop : -1.83 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 217 HIS 0.010 0.003 HIS F 57 PHE 0.032 0.003 PHE G 42 TYR 0.042 0.003 TYR C 11 ARG 0.011 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 421 time to evaluate : 2.192 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: 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: 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: A 41 PHE cc_start: 0.7388 (t80) cc_final: 0.7156 (t80) REVERT: B 234 ASN cc_start: 0.7363 (m-40) cc_final: 0.7051 (m110) REVERT: E 60 SER cc_start: 0.8791 (t) cc_final: 0.8566 (p) REVERT: I 66 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7747 (mtm110) REVERT: M 18 GLU cc_start: 0.7131 (mp0) cc_final: 0.6867 (mp0) outliers start: 9 outliers final: 6 residues processed: 427 average time/residue: 0.8817 time to fit residues: 498.3491 Evaluate side-chains 286 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 280 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain S residue 180 GLU Chi-restraints excluded: chain S residue 243 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 65 GLN A 214 ASN B 7 ASN B 214 ASN E 8 GLN E 52 GLN F 8 GLN H 48 ASN I 41 GLN J 8 GLN J 28 ASN K 8 GLN K 48 ASN L 28 ASN L 41 GLN L 48 ASN L 52 GLN N 52 GLN R 34 GLN R 214 ASN S 214 ASN ** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16115 Z= 0.197 Angle : 0.599 7.607 22023 Z= 0.311 Chirality : 0.045 0.170 2445 Planarity : 0.006 0.094 2708 Dihedral : 10.797 73.659 2532 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.77 % Allowed : 9.45 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.19), residues: 1809 helix: -1.01 (0.26), residues: 366 sheet: -1.78 (0.20), residues: 598 loop : -1.28 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 217 HIS 0.004 0.001 HIS F 57 PHE 0.020 0.001 PHE B 41 TYR 0.014 0.001 TYR B 221 ARG 0.008 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 311 time to evaluate : 2.540 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: 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: A 12 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7826 (tp-100) REVERT: A 41 PHE cc_start: 0.7350 (t80) cc_final: 0.7111 (t80) REVERT: B 35 ASP cc_start: 0.7146 (t0) cc_final: 0.6880 (t0) REVERT: B 199 ASP cc_start: 0.6508 (t0) cc_final: 0.6302 (t0) REVERT: B 234 ASN cc_start: 0.7413 (m-40) cc_final: 0.7115 (m110) REVERT: G 7 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7525 (tt) REVERT: I 37 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7601 (mt-10) REVERT: I 66 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7759 (mtm110) REVERT: J 19 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7546 (mmt90) REVERT: N 69 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.6572 (mtm-85) REVERT: R 100 ASP cc_start: 0.7516 (p0) cc_final: 0.6931 (p0) REVERT: R 101 LYS cc_start: 0.8597 (tptp) cc_final: 0.8049 (tppt) REVERT: S 142 GLU cc_start: 0.6597 (mm-30) cc_final: 0.5790 (mm-30) REVERT: S 208 GLU cc_start: 0.8117 (tp30) cc_final: 0.7790 (tp30) outliers start: 29 outliers final: 21 residues processed: 335 average time/residue: 0.8668 time to fit residues: 393.9578 Evaluate side-chains 286 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 264 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain S residue 5 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS D 8 GLN J 28 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 HIS R 12 GLN R 121 GLN ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 209 GLN ** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 16115 Z= 0.426 Angle : 0.663 7.489 22023 Z= 0.347 Chirality : 0.048 0.178 2445 Planarity : 0.006 0.092 2708 Dihedral : 10.910 73.641 2526 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.38 % Allowed : 9.93 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1809 helix: -0.20 (0.29), residues: 368 sheet: -1.63 (0.20), residues: 588 loop : -1.27 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 217 HIS 0.010 0.002 HIS R 246 PHE 0.016 0.002 PHE B 85 TYR 0.019 0.002 TYR B 221 ARG 0.007 0.001 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 265 time to evaluate : 2.436 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: A 12 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7922 (tp-100) REVERT: A 41 PHE cc_start: 0.7397 (t80) cc_final: 0.7119 (t80) REVERT: B 43 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7601 (mp) REVERT: B 83 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7652 (tt) REVERT: B 234 ASN cc_start: 0.7576 (m-40) cc_final: 0.7272 (m110) REVERT: I 31 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7869 (tttt) REVERT: I 37 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7754 (mt-10) REVERT: I 66 ARG cc_start: 0.8068 (ttp-110) cc_final: 0.7762 (mtm110) REVERT: J 19 ARG cc_start: 0.7895 (mtt90) cc_final: 0.7559 (mmt-90) REVERT: N 24 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7095 (mt) REVERT: R 41 PHE cc_start: 0.6549 (m-80) cc_final: 0.5954 (m-10) REVERT: R 100 ASP cc_start: 0.7474 (p0) cc_final: 0.6856 (p0) REVERT: R 101 LYS cc_start: 0.8622 (tptp) cc_final: 0.8107 (tppt) outliers start: 39 outliers final: 30 residues processed: 295 average time/residue: 0.8949 time to fit residues: 357.7188 Evaluate side-chains 279 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 31 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain S residue 5 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16115 Z= 0.168 Angle : 0.548 7.766 22023 Z= 0.282 Chirality : 0.044 0.171 2445 Planarity : 0.005 0.088 2708 Dihedral : 10.390 73.607 2526 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.65 % Allowed : 11.33 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 1809 helix: -0.05 (0.28), residues: 392 sheet: -1.31 (0.21), residues: 572 loop : -0.95 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 217 HIS 0.004 0.001 HIS C 57 PHE 0.012 0.001 PHE B 41 TYR 0.011 0.001 TYR B 221 ARG 0.007 0.000 ARG J 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 265 time to evaluate : 2.435 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: A 12 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7906 (tp-100) REVERT: A 41 PHE cc_start: 0.7345 (t80) cc_final: 0.7063 (t80) REVERT: B 83 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7658 (tt) REVERT: B 234 ASN cc_start: 0.7422 (m-40) cc_final: 0.7133 (m110) REVERT: B 243 PHE cc_start: 0.8598 (m-80) cc_final: 0.8213 (m-80) REVERT: I 37 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7570 (mt-10) REVERT: I 66 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7721 (mtm110) REVERT: J 19 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7657 (mmt-90) REVERT: N 24 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7034 (mt) REVERT: N 69 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.6657 (mtm-85) REVERT: R 41 PHE cc_start: 0.6501 (m-80) cc_final: 0.5921 (m-10) REVERT: R 101 LYS cc_start: 0.8585 (tptp) cc_final: 0.8146 (tppt) REVERT: S 128 ASP cc_start: 0.5938 (p0) cc_final: 0.5403 (m-30) REVERT: S 213 LEU cc_start: 0.8400 (tt) cc_final: 0.8173 (mp) outliers start: 27 outliers final: 20 residues processed: 286 average time/residue: 0.8665 time to fit residues: 337.4596 Evaluate side-chains 268 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 246 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain S residue 72 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 HIS ** R 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 214 ASN ** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16115 Z= 0.314 Angle : 0.589 6.008 22023 Z= 0.307 Chirality : 0.046 0.199 2445 Planarity : 0.005 0.087 2708 Dihedral : 10.386 73.518 2525 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.56 % Allowed : 11.15 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1809 helix: 0.03 (0.28), residues: 401 sheet: -1.21 (0.21), residues: 572 loop : -1.03 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 217 HIS 0.007 0.001 HIS H 57 PHE 0.013 0.001 PHE B 85 TYR 0.017 0.002 TYR B 221 ARG 0.006 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 255 time to evaluate : 2.401 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: A 12 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7996 (tp-100) REVERT: A 41 PHE cc_start: 0.7384 (t80) cc_final: 0.7092 (t80) REVERT: B 83 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7812 (tt) REVERT: C 37 GLU cc_start: 0.7225 (mm-30) cc_final: 0.7013 (mm-30) REVERT: C 53 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7437 (tmm) REVERT: I 31 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7856 (tttt) REVERT: I 37 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7666 (mt-10) REVERT: I 53 MET cc_start: 0.6649 (ttt) cc_final: 0.6430 (ttt) REVERT: I 66 ARG cc_start: 0.8057 (ttp-110) cc_final: 0.7746 (mtm110) REVERT: L 17 LYS cc_start: 0.7812 (mptt) cc_final: 0.7493 (mtpt) REVERT: N 24 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7033 (mt) REVERT: R 41 PHE cc_start: 0.6465 (m-80) cc_final: 0.5876 (m-10) REVERT: R 100 ASP cc_start: 0.7518 (p0) cc_final: 0.6966 (p0) REVERT: R 101 LYS cc_start: 0.8497 (tptp) cc_final: 0.8031 (tppt) REVERT: S 91 TYR cc_start: 0.7569 (m-80) cc_final: 0.7238 (m-80) REVERT: S 251 VAL cc_start: 0.5311 (OUTLIER) cc_final: 0.5010 (p) outliers start: 42 outliers final: 32 residues processed: 285 average time/residue: 0.8801 time to fit residues: 341.5428 Evaluate side-chains 281 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 244 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 31 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain S residue 5 SER Chi-restraints excluded: chain S residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN ** R 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 GLN ** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16115 Z= 0.308 Angle : 0.583 6.877 22023 Z= 0.303 Chirality : 0.046 0.226 2445 Planarity : 0.005 0.085 2708 Dihedral : 10.314 73.594 2525 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.05 % Allowed : 11.46 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1809 helix: 0.11 (0.28), residues: 401 sheet: -1.29 (0.21), residues: 586 loop : -1.03 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 217 HIS 0.006 0.001 HIS H 57 PHE 0.013 0.001 PHE B 85 TYR 0.016 0.002 TYR L 55 ARG 0.010 0.001 ARG J 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 244 time to evaluate : 2.427 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: symmetry clash REVERT: A 12 GLN cc_start: 0.8253 (tp-100) cc_final: 0.8023 (tp-100) REVERT: A 41 PHE cc_start: 0.7384 (t80) cc_final: 0.7107 (t80) REVERT: A 109 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B 83 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7884 (tt) REVERT: E 35 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: I 31 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7858 (tttt) REVERT: I 53 MET cc_start: 0.6664 (ttt) cc_final: 0.6423 (ttt) REVERT: I 66 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7737 (mtm110) REVERT: N 24 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7048 (mt) REVERT: N 69 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.6541 (mtm-85) REVERT: R 41 PHE cc_start: 0.6492 (m-80) cc_final: 0.6046 (m-10) REVERT: R 101 LYS cc_start: 0.8438 (tptp) cc_final: 0.8097 (tppt) REVERT: S 86 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7582 (tm-30) REVERT: S 91 TYR cc_start: 0.7521 (m-80) cc_final: 0.7236 (m-80) outliers start: 50 outliers final: 42 residues processed: 282 average time/residue: 0.8515 time to fit residues: 325.7949 Evaluate side-chains 284 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 237 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain D residue 5 HIS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 31 LYS Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 5 SER Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 131 HIS Chi-restraints excluded: chain S residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16115 Z= 0.224 Angle : 0.554 7.143 22023 Z= 0.286 Chirality : 0.045 0.206 2445 Planarity : 0.004 0.082 2708 Dihedral : 10.096 73.575 2525 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.74 % Allowed : 12.25 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.20), residues: 1809 helix: 0.30 (0.28), residues: 401 sheet: -1.21 (0.21), residues: 586 loop : -0.86 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.004 0.001 HIS C 57 PHE 0.010 0.001 PHE B 41 TYR 0.019 0.001 TYR S 132 ARG 0.006 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 251 time to evaluate : 2.468 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: A 12 GLN cc_start: 0.8281 (tp-100) cc_final: 0.8056 (tp-100) REVERT: A 41 PHE cc_start: 0.7363 (t80) cc_final: 0.7094 (t80) REVERT: A 211 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 83 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 234 ASN cc_start: 0.7514 (m-40) cc_final: 0.7204 (m110) REVERT: B 243 PHE cc_start: 0.8571 (m-80) cc_final: 0.8163 (m-80) REVERT: E 35 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: I 66 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7716 (mtm110) REVERT: L 17 LYS cc_start: 0.7768 (mptt) cc_final: 0.7435 (mtpt) REVERT: L 18 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6822 (tm-30) REVERT: N 24 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7049 (mt) REVERT: N 69 ARG cc_start: 0.7562 (mtp-110) cc_final: 0.6563 (mtm-85) REVERT: R 41 PHE cc_start: 0.6480 (m-80) cc_final: 0.6040 (m-10) REVERT: R 101 LYS cc_start: 0.8426 (tptp) cc_final: 0.8077 (tppt) REVERT: R 135 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7544 (tptt) REVERT: S 86 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7561 (tm-30) REVERT: S 214 ASN cc_start: 0.8131 (t0) cc_final: 0.7920 (t0) outliers start: 45 outliers final: 33 residues processed: 286 average time/residue: 0.8707 time to fit residues: 340.6338 Evaluate side-chains 280 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 244 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain D residue 5 HIS Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain S residue 5 SER Chi-restraints excluded: chain S residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.0060 chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 HIS ** R 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16115 Z= 0.205 Angle : 0.541 6.941 22023 Z= 0.278 Chirality : 0.044 0.193 2445 Planarity : 0.004 0.080 2708 Dihedral : 9.934 73.572 2525 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.74 % Allowed : 12.43 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1809 helix: 0.46 (0.28), residues: 401 sheet: -1.19 (0.21), residues: 586 loop : -0.76 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 217 HIS 0.004 0.001 HIS C 57 PHE 0.010 0.001 PHE B 85 TYR 0.017 0.001 TYR S 132 ARG 0.012 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 247 time to evaluate : 2.324 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: A 12 GLN cc_start: 0.8285 (tp-100) cc_final: 0.8069 (tp-100) REVERT: A 41 PHE cc_start: 0.7344 (t80) cc_final: 0.7081 (t80) REVERT: A 109 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7493 (mp) REVERT: A 211 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 234 ASN cc_start: 0.7494 (m-40) cc_final: 0.7129 (m-40) REVERT: B 243 PHE cc_start: 0.8557 (m-80) cc_final: 0.8345 (m-80) REVERT: L 17 LYS cc_start: 0.7769 (mptt) cc_final: 0.7464 (mtpt) REVERT: L 18 GLU cc_start: 0.7481 (tm-30) cc_final: 0.6878 (tm-30) REVERT: N 24 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7024 (mt) REVERT: N 69 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.6583 (mtm-85) REVERT: R 41 PHE cc_start: 0.6491 (m-80) cc_final: 0.6055 (m-10) REVERT: R 101 LYS cc_start: 0.8411 (tptp) cc_final: 0.8073 (tppt) REVERT: S 86 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7548 (tm-30) REVERT: S 214 ASN cc_start: 0.8162 (t0) cc_final: 0.7941 (t0) outliers start: 45 outliers final: 38 residues processed: 281 average time/residue: 0.8484 time to fit residues: 325.2764 Evaluate side-chains 281 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain D residue 5 HIS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain S residue 5 SER Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16115 Z= 0.380 Angle : 0.609 7.983 22023 Z= 0.316 Chirality : 0.047 0.236 2445 Planarity : 0.005 0.085 2708 Dihedral : 10.157 73.646 2525 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.74 % Allowed : 12.74 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.20), residues: 1809 helix: 0.39 (0.28), residues: 401 sheet: -1.21 (0.21), residues: 586 loop : -0.91 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 217 HIS 0.007 0.002 HIS R 131 PHE 0.015 0.001 PHE C 42 TYR 0.021 0.002 TYR L 55 ARG 0.006 0.001 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 242 time to evaluate : 2.693 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: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8340 (tp-100) cc_final: 0.8104 (tp-100) REVERT: A 41 PHE cc_start: 0.7371 (t80) cc_final: 0.7114 (t80) REVERT: A 109 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7584 (mp) REVERT: A 211 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7654 (tm-30) REVERT: C 46 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7830 (tp) REVERT: E 35 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: L 17 LYS cc_start: 0.7797 (mptt) cc_final: 0.7476 (mtpt) REVERT: N 24 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7078 (mt) REVERT: R 41 PHE cc_start: 0.6722 (m-80) cc_final: 0.6276 (m-10) REVERT: R 101 LYS cc_start: 0.8421 (tptp) cc_final: 0.8088 (tppt) REVERT: R 135 LYS cc_start: 0.7878 (ttmm) cc_final: 0.7509 (tptt) REVERT: S 86 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7536 (tm-30) outliers start: 45 outliers final: 39 residues processed: 276 average time/residue: 0.8454 time to fit residues: 314.1865 Evaluate side-chains 282 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 5 HIS Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain S residue 5 SER Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 131 HIS Chi-restraints excluded: chain S residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 150 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 HIS ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16115 Z= 0.162 Angle : 0.531 7.300 22023 Z= 0.272 Chirality : 0.044 0.226 2445 Planarity : 0.004 0.079 2708 Dihedral : 9.762 73.670 2525 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.58 % Allowed : 13.65 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1809 helix: 0.63 (0.28), residues: 401 sheet: -1.13 (0.21), residues: 587 loop : -0.62 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.003 0.001 HIS B 246 PHE 0.011 0.001 PHE B 41 TYR 0.018 0.001 TYR S 132 ARG 0.009 0.000 ARG C 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 251 time to evaluate : 2.217 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: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8277 (tp-100) cc_final: 0.8072 (tp-100) REVERT: A 41 PHE cc_start: 0.7269 (t80) cc_final: 0.7026 (t80) REVERT: A 211 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 234 ASN cc_start: 0.7477 (m-40) cc_final: 0.7126 (m-40) REVERT: B 243 PHE cc_start: 0.8528 (m-80) cc_final: 0.8104 (m-80) REVERT: C 46 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7820 (tp) REVERT: J 33 GLN cc_start: 0.7967 (mp10) cc_final: 0.7570 (mp10) REVERT: L 17 LYS cc_start: 0.7842 (mptt) cc_final: 0.7530 (mtpt) REVERT: L 18 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6870 (tm-30) REVERT: N 24 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7042 (mt) REVERT: N 69 ARG cc_start: 0.7393 (mtp-110) cc_final: 0.6440 (mtm-85) REVERT: R 41 PHE cc_start: 0.6712 (m-80) cc_final: 0.6322 (m-10) REVERT: R 101 LYS cc_start: 0.8396 (tptp) cc_final: 0.8059 (tppt) REVERT: S 35 ASP cc_start: 0.6891 (t70) cc_final: 0.6549 (t70) REVERT: S 86 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7555 (tm-30) outliers start: 26 outliers final: 20 residues processed: 269 average time/residue: 0.8457 time to fit residues: 309.7147 Evaluate side-chains 270 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain S residue 5 SER Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.128808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099913 restraints weight = 71523.812| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.02 r_work: 0.3222 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16115 Z= 0.206 Angle : 0.542 8.479 22023 Z= 0.278 Chirality : 0.044 0.230 2445 Planarity : 0.004 0.080 2708 Dihedral : 9.708 73.588 2523 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.71 % Allowed : 13.77 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1809 helix: 0.59 (0.28), residues: 405 sheet: -1.12 (0.21), residues: 587 loop : -0.54 (0.24), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.004 0.001 HIS C 57 PHE 0.010 0.001 PHE B 41 TYR 0.017 0.001 TYR S 132 ARG 0.009 0.000 ARG C 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8170.15 seconds wall clock time: 145 minutes 25.32 seconds (8725.32 seconds total)