Starting phenix.real_space_refine on Fri Apr 12 20:37:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1l_0591/04_2024/6o1l_0591_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1l_0591/04_2024/6o1l_0591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1l_0591/04_2024/6o1l_0591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1l_0591/04_2024/6o1l_0591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1l_0591/04_2024/6o1l_0591_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1l_0591/04_2024/6o1l_0591_neut.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.055 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 39 5.16 5 C 8544 2.51 5 N 2405 2.21 5 O 2531 1.98 5 H 13324 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 ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I 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 "M ARG 16": "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" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26877 Number of models: 1 Model: "" Number of chains: 17 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} Time building chain proxies: 11.90, per 1000 atoms: 0.44 Number of scatterers: 26877 At special positions: 0 Unit cell: (100.28, 131.89, 116.63, 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 39 16.00 P 34 15.00 O 2531 8.00 N 2405 7.00 C 8544 6.00 H 13324 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: 21.63 Conformation dependent library (CDL) restraints added in 2.5 seconds 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3002 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 11 sheets defined 23.7% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.05 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.593A pdb=" N VAL A 158 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.995A pdb=" N GLN A 165 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 182 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.246A pdb=" N VAL A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 195' Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.692A pdb=" N LEU A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.562A 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 16 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.752A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.505A pdb=" N ASP B 45 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.579A pdb=" N ASP B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 90' Processing helix chain 'B' and resid 115 through 136 removed outlier: 3.877A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 171 through 184 removed outlier: 3.769A pdb=" N TRP B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 226 through 229 removed outlier: 3.807A 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 8 through 18 Processing helix chain 'D' and resid 7 through 18 removed outlier: 3.502A pdb=" N GLU D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 18 removed outlier: 3.785A pdb=" N GLU E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 18 removed outlier: 3.989A pdb=" N GLU F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.230A pdb=" N TYR G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 18 removed outlier: 3.629A pdb=" N TYR H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 18 removed outlier: 3.819A pdb=" N TYR I 11 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU I 18 " --> pdb=" O THR I 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 18 removed outlier: 3.620A pdb=" N TYR J 11 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU J 18 " --> pdb=" O THR J 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 18 removed outlier: 3.710A pdb=" N TYR K 11 " --> pdb=" O LEU K 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU K 18 " --> pdb=" O THR K 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 18 removed outlier: 3.570A pdb=" N GLU L 18 " --> pdb=" O THR L 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 18 Processing helix chain 'N' and resid 7 through 17 removed outlier: 3.621A pdb=" N TYR N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU N 15 " --> pdb=" O TYR N 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 15 Processing helix chain 'R' and resid 19 through 27 removed outlier: 3.928A pdb=" N ALA R 25 " --> pdb=" O SER R 21 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN R 27 " --> pdb=" O LEU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 90 removed outlier: 3.643A pdb=" N ARG R 90 " --> pdb=" O GLU R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 137 removed outlier: 3.508A pdb=" N LEU R 119 " --> pdb=" O GLY R 115 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS R 135 " --> pdb=" O HIS R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 158 Processing helix chain 'R' and resid 160 through 165 removed outlier: 3.501A pdb=" N CYS R 164 " --> pdb=" O ASN R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 185 removed outlier: 3.852A pdb=" N ASN R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 removed outlier: 6.604A pdb=" N ARG A 2 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS A 32 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 4 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 250 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 235 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP A 252 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 7.110A pdb=" N SER A 103 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N CYS A 146 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA A 105 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N SER A 148 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.442A 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: 6.713A pdb=" N ARG B 2 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N CYS B 32 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE B 4 " --> pdb=" O CYS B 32 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 250 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA B 235 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP B 252 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 81 removed outlier: 6.908A pdb=" N SER B 103 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N CYS B 146 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA B 105 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER B 148 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 107 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 64 removed outlier: 7.316A pdb=" N LEU C 45 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE C 39 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL C 43 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N SER C 51 " --> pdb=" O PRO D 64 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER D 60 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 61 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE D 36 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS D 47 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER D 38 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR D 55 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER E 60 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR E 25 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL E 62 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER E 23 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.682A pdb=" N SER E 51 " --> pdb=" O PRO F 64 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER F 60 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU F 45 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE F 39 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER F 51 " --> pdb=" O PRO H 64 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER H 60 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR H 25 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL H 62 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER H 23 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE H 36 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS H 47 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER H 38 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER H 51 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER G 60 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR G 25 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL G 62 " --> pdb=" O SER G 23 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER G 23 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU G 45 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE G 39 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL G 43 " --> pdb=" O PHE G 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 31 through 34 removed outlier: 6.728A pdb=" N SER I 23 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL I 62 " --> pdb=" O SER I 23 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR I 25 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER I 60 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL N 43 " --> pdb=" O PHE N 39 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE N 39 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU N 45 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR N 61 " --> pdb=" O TYR N 25 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER N 60 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER M 38 " --> pdb=" O LEU M 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 43 through 46 removed outlier: 6.794A pdb=" N SER J 60 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU J 45 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE J 39 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL J 43 " --> pdb=" O PHE J 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 59 through 64 removed outlier: 6.962A pdb=" N TYR K 25 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL K 62 " --> pdb=" O SER K 23 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER K 23 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU K 45 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE K 39 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL K 43 " --> pdb=" O PHE K 39 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER K 51 " --> pdb=" O PRO L 64 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER L 60 " --> pdb=" O TYR K 55 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE L 36 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS L 47 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N SER L 51 " --> pdb=" O PRO M 64 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER M 60 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR M 25 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL M 62 " --> pdb=" O SER M 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER M 23 " --> pdb=" O VAL M 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 54 through 58 Processing sheet with id=AB2, first strand: chain 'R' and resid 78 through 81 removed outlier: 3.671A pdb=" N SER R 103 " --> pdb=" O GLU R 142 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1284 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: 10.58 Time building geometry restraints manager: 22.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 3155 1.02 - 1.22: 10167 1.22 - 1.41: 5862 1.41 - 1.61: 8004 1.61 - 1.81: 74 Bond restraints: 27262 Sorted by residual: bond pdb=" NH2 ARG A 140 " pdb="HH21 ARG A 140 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ASN R 214 " pdb=" H ASN R 214 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ARG M 16 " pdb=" H ARG M 16 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LEU D 26 " pdb=" H LEU D 26 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE3 TRP R 255 " pdb=" HE3 TRP R 255 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 27257 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.68: 616 105.68 - 113.50: 31474 113.50 - 121.33: 13144 121.33 - 129.15: 3896 129.15 - 136.98: 140 Bond angle restraints: 49270 Sorted by residual: angle pdb=" C6 A P 10 " pdb=" N6 A P 10 " pdb=" H61 A P 10 " ideal model delta sigma weight residual 120.00 98.99 21.01 3.00e+00 1.11e-01 4.90e+01 angle pdb=" N PHE R 243 " pdb=" CA PHE R 243 " pdb=" C PHE R 243 " ideal model delta sigma weight residual 112.92 120.17 -7.25 1.23e+00 6.61e-01 3.47e+01 angle pdb=" C6 A P 7 " pdb=" N6 A P 7 " pdb=" H61 A P 7 " ideal model delta sigma weight residual 120.00 103.53 16.47 3.00e+00 1.11e-01 3.02e+01 angle pdb=" C GLN B 240 " pdb=" N PRO B 241 " pdb=" CA PRO B 241 " ideal model delta sigma weight residual 120.96 113.45 7.51 1.41e+00 5.03e-01 2.84e+01 angle pdb=" C6 A O 4 " pdb=" N6 A O 4 " pdb=" H61 A O 4 " ideal model delta sigma weight residual 120.00 105.79 14.21 3.00e+00 1.11e-01 2.24e+01 ... (remaining 49265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11520 17.99 - 35.97: 628 35.97 - 53.96: 259 53.96 - 71.94: 307 71.94 - 89.93: 36 Dihedral angle restraints: 12750 sinusoidal: 7278 harmonic: 5472 Sorted by residual: 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 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LEU R 62 " pdb=" C LEU R 62 " pdb=" N PRO R 63 " pdb=" CA PRO R 63 " ideal model delta harmonic sigma weight residual -180.00 -155.09 -24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA HIS E 5 " pdb=" C HIS E 5 " pdb=" N SER E 6 " pdb=" CA SER E 6 " ideal model delta harmonic sigma weight residual -180.00 -155.54 -24.46 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 12747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1834 0.101 - 0.201: 281 0.201 - 0.302: 27 0.302 - 0.402: 2 0.402 - 0.503: 1 Chirality restraints: 2145 Sorted by residual: chirality pdb=" CG LEU A 133 " pdb=" CB LEU A 133 " pdb=" CD1 LEU A 133 " pdb=" CD2 LEU A 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" CG LEU M 15 " pdb=" CB LEU M 15 " pdb=" CD1 LEU M 15 " pdb=" CD2 LEU M 15 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA PHE R 243 " pdb=" N PHE R 243 " pdb=" C PHE R 243 " pdb=" CB PHE R 243 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 2142 not shown) Planarity restraints: 3825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 240 " -0.211 2.00e-02 2.50e+03 2.44e-01 8.94e+02 pdb=" CD GLN R 240 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN R 240 " 0.208 2.00e-02 2.50e+03 pdb=" NE2 GLN R 240 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN R 240 " 0.365 2.00e-02 2.50e+03 pdb="HE22 GLN R 240 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 A P 7 " -0.071 2.00e-02 2.50e+03 1.68e-01 2.83e+02 pdb=" N6 A P 7 " 0.290 2.00e-02 2.50e+03 pdb=" H61 A P 7 " -0.105 2.00e-02 2.50e+03 pdb=" H62 A P 7 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 A O 10 " 0.071 2.00e-02 2.50e+03 1.59e-01 2.54e+02 pdb=" N6 A O 10 " -0.275 2.00e-02 2.50e+03 pdb=" H61 A O 10 " 0.102 2.00e-02 2.50e+03 pdb=" H62 A O 10 " 0.102 2.00e-02 2.50e+03 ... (remaining 3822 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.85: 412 1.85 - 2.54: 23005 2.54 - 3.23: 79340 3.23 - 3.91: 109907 3.91 - 4.60: 166960 Nonbonded interactions: 379624 Sorted by model distance: nonbonded pdb=" HA PHE E 42 " pdb=" HD3 LYS E 56 " model vdw 1.166 2.440 nonbonded pdb=" HG SER C 60 " pdb=" H THR C 61 " model vdw 1.238 2.100 nonbonded pdb=" O PHE A 99 " pdb="HH22 ARG A 141 " model vdw 1.347 1.850 nonbonded pdb="HE21 GLN A 75 " pdb=" HB THR K 49 " model vdw 1.361 2.270 nonbonded pdb=" HZ2 TRP R 204 " pdb=" HD3 ARG R 239 " model vdw 1.390 2.270 ... (remaining 379619 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' } 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: 0.350 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: 0.340 Extract box with map and model: 2.980 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 93.970 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.010 0.110 13938 Z= 0.664 Angle : 1.193 16.218 19075 Z= 0.666 Chirality : 0.072 0.503 2145 Planarity : 0.008 0.076 2317 Dihedral : 12.864 86.912 5401 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.04 % Favored : 92.83 % Rotamer: Outliers : 1.20 % Allowed : 5.77 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.18), residues: 1549 helix: -3.37 (0.18), residues: 330 sheet: -2.53 (0.21), residues: 487 loop : -1.86 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 217 HIS 0.016 0.004 HIS H 57 PHE 0.032 0.004 PHE F 42 TYR 0.081 0.004 TYR F 55 ARG 0.011 0.001 ARG I 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 334 time to evaluate : 2.135 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: B 68 VAL cc_start: 0.8903 (t) cc_final: 0.8678 (p) REVERT: B 202 SER cc_start: 0.8326 (m) cc_final: 0.7842 (t) REVERT: C 33 GLN cc_start: 0.7672 (pt0) cc_final: 0.7442 (pt0) REVERT: E 41 GLN cc_start: 0.7044 (tm-30) cc_final: 0.6549 (tm-30) REVERT: G 19 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7623 (mmt180) REVERT: G 47 LYS cc_start: 0.8136 (tttp) cc_final: 0.7812 (tttp) REVERT: J 37 GLU cc_start: 0.8093 (tp30) cc_final: 0.7852 (mm-30) REVERT: K 65 SER cc_start: 0.8110 (m) cc_final: 0.7854 (m) REVERT: L 11 TYR cc_start: 0.8616 (t80) cc_final: 0.8274 (t80) REVERT: R 9 ASN cc_start: 0.6694 (m110) cc_final: 0.6491 (m-40) REVERT: R 77 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8332 (mtmm) outliers start: 17 outliers final: 6 residues processed: 345 average time/residue: 0.8492 time to fit residues: 393.2039 Evaluate side-chains 261 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 255 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 242 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN A 214 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 136 GLN B 214 ASN C 5 HIS D 35 GLN E 48 ASN F 57 HIS G 57 HIS H 48 ASN H 57 HIS I 8 GLN I 52 GLN J 8 GLN K 8 GLN K 48 ASN L 52 GLN N 52 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 222 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13938 Z= 0.199 Angle : 0.630 6.952 19075 Z= 0.325 Chirality : 0.047 0.164 2145 Planarity : 0.006 0.053 2317 Dihedral : 11.460 88.660 2242 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.77 % Rotamer: Outliers : 1.90 % Allowed : 9.23 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.20), residues: 1549 helix: -1.83 (0.26), residues: 335 sheet: -2.14 (0.21), residues: 483 loop : -1.23 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 217 HIS 0.007 0.001 HIS R 246 PHE 0.015 0.002 PHE A 41 TYR 0.010 0.001 TYR A 150 ARG 0.004 0.001 ARG I 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 290 time to evaluate : 2.151 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: A 62 LEU cc_start: 0.8893 (mt) cc_final: 0.8645 (mm) REVERT: B 202 SER cc_start: 0.8378 (m) cc_final: 0.7847 (t) REVERT: C 11 TYR cc_start: 0.6643 (t80) cc_final: 0.6391 (t80) REVERT: C 13 ASN cc_start: 0.7532 (t0) cc_final: 0.7328 (m-40) REVERT: C 16 ARG cc_start: 0.7949 (tmm-80) cc_final: 0.7567 (tmm-80) REVERT: C 35 GLN cc_start: 0.8140 (mt0) cc_final: 0.7752 (mt0) REVERT: C 39 PHE cc_start: 0.7591 (p90) cc_final: 0.7292 (p90) REVERT: E 41 GLN cc_start: 0.7537 (tm-30) cc_final: 0.6940 (tm-30) REVERT: G 19 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7588 (mmt180) REVERT: G 47 LYS cc_start: 0.8464 (tttp) cc_final: 0.8228 (tptm) REVERT: H 41 GLN cc_start: 0.7782 (mp10) cc_final: 0.7012 (mp10) REVERT: H 42 PHE cc_start: 0.7883 (m-10) cc_final: 0.7598 (m-10) REVERT: I 19 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7826 (mtt-85) REVERT: J 19 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7361 (tpp80) REVERT: J 37 GLU cc_start: 0.8208 (tp30) cc_final: 0.7900 (mm-30) REVERT: K 37 GLU cc_start: 0.7743 (mp0) cc_final: 0.7015 (mp0) REVERT: K 40 ASP cc_start: 0.8162 (p0) cc_final: 0.7483 (p0) REVERT: K 65 SER cc_start: 0.7960 (m) cc_final: 0.7658 (m) REVERT: L 11 TYR cc_start: 0.8484 (t80) cc_final: 0.8221 (t80) REVERT: M 39 PHE cc_start: 0.6970 (p90) cc_final: 0.6566 (p90) REVERT: R 9 ASN cc_start: 0.6719 (m110) cc_final: 0.6296 (m-40) REVERT: R 77 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8509 (mtmm) REVERT: R 242 ARG cc_start: 0.4469 (OUTLIER) cc_final: 0.3636 (ptm-80) REVERT: R 256 GLN cc_start: 0.6663 (mp10) cc_final: 0.6372 (mp10) outliers start: 27 outliers final: 18 residues processed: 303 average time/residue: 0.7820 time to fit residues: 326.1857 Evaluate side-chains 280 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 261 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 42 PHE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 242 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN D 35 GLN G 8 GLN G 52 GLN I 48 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 13938 Z= 0.381 Angle : 0.647 6.803 19075 Z= 0.334 Chirality : 0.048 0.173 2145 Planarity : 0.005 0.050 2317 Dihedral : 11.246 92.873 2240 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.89 % Allowed : 11.48 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.21), residues: 1549 helix: -1.16 (0.28), residues: 330 sheet: -2.05 (0.22), residues: 484 loop : -1.09 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 217 HIS 0.010 0.002 HIS R 246 PHE 0.014 0.002 PHE R 201 TYR 0.015 0.002 TYR A 150 ARG 0.005 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 260 time to evaluate : 2.110 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: A 62 LEU cc_start: 0.8905 (mt) cc_final: 0.8656 (mm) REVERT: A 191 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8796 (tp) REVERT: C 7 LEU cc_start: 0.7695 (tt) cc_final: 0.7335 (tp) REVERT: C 11 TYR cc_start: 0.6746 (t80) cc_final: 0.6503 (t80) REVERT: C 35 GLN cc_start: 0.8299 (mt0) cc_final: 0.8078 (mt0) REVERT: C 56 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7983 (mtpp) REVERT: E 9 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7562 (p0) REVERT: E 31 LYS cc_start: 0.8238 (ptpt) cc_final: 0.7984 (pttt) REVERT: E 41 GLN cc_start: 0.7591 (tm-30) cc_final: 0.6942 (tm-30) REVERT: G 8 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: G 19 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7617 (mmt180) REVERT: J 37 GLU cc_start: 0.8305 (tp30) cc_final: 0.8013 (mm-30) REVERT: K 37 GLU cc_start: 0.7703 (mp0) cc_final: 0.6847 (mp0) REVERT: K 40 ASP cc_start: 0.8261 (p0) cc_final: 0.7576 (p0) REVERT: K 65 SER cc_start: 0.7889 (m) cc_final: 0.7562 (m) REVERT: M 39 PHE cc_start: 0.7376 (p90) cc_final: 0.6860 (p90) REVERT: R 9 ASN cc_start: 0.6843 (m110) cc_final: 0.6538 (m-40) REVERT: R 77 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8356 (mtmm) REVERT: R 101 LYS cc_start: 0.8805 (tptt) cc_final: 0.8438 (tptt) REVERT: R 221 TYR cc_start: 0.6602 (m-10) cc_final: 0.6342 (m-10) REVERT: R 242 ARG cc_start: 0.4444 (OUTLIER) cc_final: 0.3759 (ptm-80) REVERT: R 256 GLN cc_start: 0.6707 (mp10) cc_final: 0.6390 (mp10) outliers start: 41 outliers final: 28 residues processed: 285 average time/residue: 0.7773 time to fit residues: 301.1832 Evaluate side-chains 276 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 244 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 40 ASP Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 28 ASN Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 242 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN I 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13938 Z= 0.326 Angle : 0.606 6.317 19075 Z= 0.311 Chirality : 0.047 0.167 2145 Planarity : 0.005 0.051 2317 Dihedral : 11.083 92.716 2239 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.82 % Allowed : 12.39 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.21), residues: 1549 helix: -0.86 (0.29), residues: 330 sheet: -1.86 (0.22), residues: 472 loop : -0.99 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 217 HIS 0.009 0.001 HIS R 246 PHE 0.011 0.001 PHE R 41 TYR 0.015 0.002 TYR L 11 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 240 time to evaluate : 2.087 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: A 62 LEU cc_start: 0.8835 (mt) cc_final: 0.8628 (mm) REVERT: A 175 ARG cc_start: 0.8477 (mtp-110) cc_final: 0.8119 (mtp85) REVERT: A 180 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7343 (tm-30) REVERT: C 37 GLU cc_start: 0.7904 (tt0) cc_final: 0.7222 (mt-10) REVERT: E 31 LYS cc_start: 0.8192 (ptpt) cc_final: 0.7977 (pttt) REVERT: E 41 GLN cc_start: 0.7547 (tm-30) cc_final: 0.6912 (tm-30) REVERT: G 19 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7622 (mmt180) REVERT: J 37 GLU cc_start: 0.8328 (tp30) cc_final: 0.8033 (mm-30) REVERT: K 37 GLU cc_start: 0.7760 (mp0) cc_final: 0.6886 (mp0) REVERT: K 40 ASP cc_start: 0.8235 (p0) cc_final: 0.7556 (p0) REVERT: K 65 SER cc_start: 0.8044 (m) cc_final: 0.7720 (m) REVERT: M 33 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: M 39 PHE cc_start: 0.7408 (p90) cc_final: 0.6840 (p90) REVERT: R 9 ASN cc_start: 0.6830 (m110) cc_final: 0.6540 (m-40) REVERT: R 77 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8342 (mtmm) REVERT: R 221 TYR cc_start: 0.6580 (m-10) cc_final: 0.6334 (m-10) REVERT: R 242 ARG cc_start: 0.4527 (OUTLIER) cc_final: 0.3925 (ptm-80) REVERT: R 256 GLN cc_start: 0.6654 (mp10) cc_final: 0.6324 (mp10) outliers start: 40 outliers final: 29 residues processed: 263 average time/residue: 0.7999 time to fit residues: 284.1597 Evaluate side-chains 267 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 28 ASN Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 242 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN D 57 HIS ** R 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13938 Z= 0.256 Angle : 0.576 6.600 19075 Z= 0.292 Chirality : 0.046 0.168 2145 Planarity : 0.005 0.049 2317 Dihedral : 10.861 92.199 2239 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.89 % Allowed : 12.89 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.21), residues: 1549 helix: -0.48 (0.30), residues: 328 sheet: -1.70 (0.23), residues: 472 loop : -0.83 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 217 HIS 0.008 0.001 HIS R 246 PHE 0.013 0.001 PHE A 41 TYR 0.012 0.001 TYR L 11 ARG 0.004 0.000 ARG L 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 240 time to evaluate : 2.487 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: A 175 ARG cc_start: 0.8436 (mtp-110) cc_final: 0.8232 (mtp85) REVERT: A 180 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7217 (tm-30) REVERT: C 9 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: E 9 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7538 (p0) REVERT: E 31 LYS cc_start: 0.8159 (ptpt) cc_final: 0.7943 (pttt) REVERT: E 41 GLN cc_start: 0.7534 (tm-30) cc_final: 0.6990 (tm-30) REVERT: F 65 SER cc_start: 0.8635 (t) cc_final: 0.8037 (p) REVERT: G 19 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7636 (mmt180) REVERT: G 47 LYS cc_start: 0.8552 (tptp) cc_final: 0.7880 (tptm) REVERT: J 37 GLU cc_start: 0.8338 (tp30) cc_final: 0.8086 (mm-30) REVERT: K 18 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: K 37 GLU cc_start: 0.7745 (mp0) cc_final: 0.6752 (mp0) REVERT: K 40 ASP cc_start: 0.8168 (p0) cc_final: 0.7529 (p0) REVERT: K 65 SER cc_start: 0.8078 (m) cc_final: 0.7737 (m) REVERT: M 33 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: M 39 PHE cc_start: 0.7490 (p90) cc_final: 0.6953 (p90) REVERT: R 9 ASN cc_start: 0.6785 (m110) cc_final: 0.6517 (m-40) REVERT: R 77 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8302 (ttpp) REVERT: R 256 GLN cc_start: 0.6717 (mp10) cc_final: 0.6388 (mp10) outliers start: 41 outliers final: 29 residues processed: 266 average time/residue: 0.7775 time to fit residues: 279.4632 Evaluate side-chains 268 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 28 ASN Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 250 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13938 Z= 0.305 Angle : 0.583 5.948 19075 Z= 0.297 Chirality : 0.046 0.170 2145 Planarity : 0.005 0.048 2317 Dihedral : 10.782 92.919 2232 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.54 % Allowed : 14.01 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.22), residues: 1549 helix: -0.41 (0.30), residues: 330 sheet: -1.67 (0.23), residues: 472 loop : -0.73 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 217 HIS 0.009 0.001 HIS R 246 PHE 0.013 0.001 PHE R 41 TYR 0.018 0.002 TYR R 91 ARG 0.006 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 240 time to evaluate : 2.387 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: A 175 ARG cc_start: 0.8416 (mtp-110) cc_final: 0.8207 (mtp85) REVERT: A 180 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7230 (tm-30) REVERT: B 35 ASP cc_start: 0.7981 (t0) cc_final: 0.7760 (t70) REVERT: E 9 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7427 (p0) REVERT: E 31 LYS cc_start: 0.8163 (ptpt) cc_final: 0.7959 (pttt) REVERT: E 41 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7072 (tm-30) REVERT: F 65 SER cc_start: 0.8576 (t) cc_final: 0.7983 (p) REVERT: G 19 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7605 (mmt180) REVERT: J 37 GLU cc_start: 0.8358 (tp30) cc_final: 0.8099 (mm-30) REVERT: K 18 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: K 37 GLU cc_start: 0.7721 (mp0) cc_final: 0.6744 (mp0) REVERT: K 40 ASP cc_start: 0.8150 (p0) cc_final: 0.7525 (p0) REVERT: K 65 SER cc_start: 0.8117 (m) cc_final: 0.7786 (m) REVERT: L 11 TYR cc_start: 0.8464 (t80) cc_final: 0.8138 (t80) REVERT: M 33 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: R 9 ASN cc_start: 0.6833 (m110) cc_final: 0.6556 (m-40) REVERT: R 77 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8310 (ttpp) REVERT: R 256 GLN cc_start: 0.6687 (mp10) cc_final: 0.6362 (mp10) outliers start: 36 outliers final: 27 residues processed: 262 average time/residue: 0.7903 time to fit residues: 284.8873 Evaluate side-chains 262 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 28 ASN Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 225 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 0.0470 chunk 91 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN ** R 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13938 Z= 0.151 Angle : 0.530 8.527 19075 Z= 0.267 Chirality : 0.044 0.159 2145 Planarity : 0.004 0.046 2317 Dihedral : 10.541 92.277 2232 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.04 % Allowed : 14.72 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.22), residues: 1549 helix: -0.18 (0.30), residues: 336 sheet: -1.41 (0.23), residues: 468 loop : -0.56 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 22 HIS 0.009 0.001 HIS R 246 PHE 0.016 0.001 PHE A 41 TYR 0.011 0.001 TYR L 11 ARG 0.007 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 246 time to evaluate : 1.924 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: A 180 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7137 (tm-30) REVERT: B 180 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6392 (tp30) REVERT: C 7 LEU cc_start: 0.7348 (tt) cc_final: 0.6823 (tp) REVERT: E 9 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7328 (p0) REVERT: E 41 GLN cc_start: 0.7514 (tm-30) cc_final: 0.6965 (tm-30) REVERT: F 65 SER cc_start: 0.8658 (t) cc_final: 0.8038 (p) REVERT: G 19 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7648 (mmt180) REVERT: H 41 GLN cc_start: 0.7744 (mp10) cc_final: 0.7040 (mp10) REVERT: J 37 GLU cc_start: 0.8334 (tp30) cc_final: 0.8072 (mm-30) REVERT: K 37 GLU cc_start: 0.7647 (mp0) cc_final: 0.6700 (mp0) REVERT: K 40 ASP cc_start: 0.7911 (p0) cc_final: 0.7220 (p0) REVERT: K 65 SER cc_start: 0.8060 (m) cc_final: 0.7756 (m) REVERT: L 11 TYR cc_start: 0.8491 (t80) cc_final: 0.8179 (t80) REVERT: L 16 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6774 (ttp80) REVERT: M 33 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7782 (mp10) REVERT: R 9 ASN cc_start: 0.6706 (m110) cc_final: 0.6461 (m-40) REVERT: R 77 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8397 (ttpp) REVERT: R 256 GLN cc_start: 0.6594 (mp10) cc_final: 0.6279 (mp10) outliers start: 29 outliers final: 21 residues processed: 262 average time/residue: 0.7921 time to fit residues: 283.9386 Evaluate side-chains 263 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 225 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13938 Z= 0.321 Angle : 0.577 5.748 19075 Z= 0.294 Chirality : 0.046 0.170 2145 Planarity : 0.005 0.046 2317 Dihedral : 10.629 93.250 2232 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.54 % Allowed : 14.86 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.22), residues: 1549 helix: -0.14 (0.30), residues: 334 sheet: -1.42 (0.23), residues: 466 loop : -0.59 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.007 0.001 HIS D 57 PHE 0.012 0.001 PHE R 41 TYR 0.012 0.002 TYR A 221 ARG 0.006 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 242 time to evaluate : 2.143 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: A 180 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 35 ASP cc_start: 0.7996 (t0) cc_final: 0.7754 (t70) REVERT: E 9 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7428 (p0) REVERT: E 41 GLN cc_start: 0.7595 (tm-30) cc_final: 0.6994 (tm-30) REVERT: F 65 SER cc_start: 0.8616 (t) cc_final: 0.8052 (p) REVERT: G 19 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7616 (mmt180) REVERT: J 37 GLU cc_start: 0.8376 (tp30) cc_final: 0.8109 (mm-30) REVERT: K 18 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: K 37 GLU cc_start: 0.7641 (mp0) cc_final: 0.6696 (mp0) REVERT: K 40 ASP cc_start: 0.7932 (p0) cc_final: 0.7290 (p0) REVERT: K 65 SER cc_start: 0.8141 (m) cc_final: 0.7837 (m) REVERT: L 11 TYR cc_start: 0.8512 (t80) cc_final: 0.8168 (t80) REVERT: L 16 ARG cc_start: 0.7384 (ttp80) cc_final: 0.6777 (ttp80) REVERT: M 33 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7723 (mp10) REVERT: R 9 ASN cc_start: 0.6842 (m110) cc_final: 0.6580 (m-40) REVERT: R 77 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8323 (ttpp) REVERT: R 256 GLN cc_start: 0.6687 (mp10) cc_final: 0.6346 (mp10) outliers start: 36 outliers final: 26 residues processed: 267 average time/residue: 0.7503 time to fit residues: 274.9844 Evaluate side-chains 269 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 240 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 225 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13938 Z= 0.211 Angle : 0.546 7.808 19075 Z= 0.275 Chirality : 0.045 0.165 2145 Planarity : 0.004 0.049 2317 Dihedral : 10.549 92.834 2232 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.11 % Allowed : 15.28 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1549 helix: -0.01 (0.30), residues: 334 sheet: -1.43 (0.23), residues: 478 loop : -0.41 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 22 HIS 0.008 0.001 HIS R 246 PHE 0.015 0.001 PHE A 41 TYR 0.011 0.001 TYR L 11 ARG 0.006 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 2.161 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: A 180 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7192 (tm-30) REVERT: E 9 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7359 (p0) REVERT: E 41 GLN cc_start: 0.7479 (tm-30) cc_final: 0.6909 (tm-30) REVERT: F 65 SER cc_start: 0.8614 (t) cc_final: 0.8062 (p) REVERT: G 19 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7614 (mmt180) REVERT: J 37 GLU cc_start: 0.8369 (tp30) cc_final: 0.8097 (mm-30) REVERT: K 37 GLU cc_start: 0.7641 (mp0) cc_final: 0.6705 (mp0) REVERT: K 40 ASP cc_start: 0.7885 (p0) cc_final: 0.7247 (p0) REVERT: K 65 SER cc_start: 0.8138 (m) cc_final: 0.7850 (m) REVERT: L 11 TYR cc_start: 0.8498 (t80) cc_final: 0.8224 (t80) REVERT: L 16 ARG cc_start: 0.7348 (ttp80) cc_final: 0.6774 (ttp80) REVERT: M 33 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: R 9 ASN cc_start: 0.6756 (m110) cc_final: 0.6503 (m-40) REVERT: R 77 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8398 (ttpp) REVERT: R 256 GLN cc_start: 0.6635 (mp10) cc_final: 0.6251 (mp10) outliers start: 30 outliers final: 26 residues processed: 263 average time/residue: 0.7574 time to fit residues: 273.8405 Evaluate side-chains 267 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 13938 Z= 0.419 Angle : 0.619 6.006 19075 Z= 0.317 Chirality : 0.048 0.169 2145 Planarity : 0.005 0.051 2317 Dihedral : 10.771 94.132 2232 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.32 % Allowed : 15.35 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1549 helix: -0.09 (0.30), residues: 328 sheet: -1.61 (0.23), residues: 486 loop : -0.51 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 217 HIS 0.008 0.001 HIS D 57 PHE 0.014 0.002 PHE J 39 TYR 0.014 0.002 TYR A 71 ARG 0.006 0.001 ARG J 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 2.120 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: A 180 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 91 TYR cc_start: 0.8708 (m-80) cc_final: 0.8360 (m-80) REVERT: E 9 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7629 (p0) REVERT: E 41 GLN cc_start: 0.7652 (tm130) cc_final: 0.7063 (tm-30) REVERT: F 65 SER cc_start: 0.8623 (t) cc_final: 0.7980 (p) REVERT: G 19 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7579 (mmt180) REVERT: J 37 GLU cc_start: 0.8401 (tp30) cc_final: 0.8141 (mm-30) REVERT: K 18 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: K 37 GLU cc_start: 0.7710 (mp0) cc_final: 0.6754 (mp0) REVERT: K 40 ASP cc_start: 0.8003 (p0) cc_final: 0.7397 (p0) REVERT: K 65 SER cc_start: 0.8172 (m) cc_final: 0.7868 (m) REVERT: L 11 TYR cc_start: 0.8511 (t80) cc_final: 0.8210 (t80) REVERT: M 33 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: R 9 ASN cc_start: 0.6905 (m110) cc_final: 0.6629 (m-40) REVERT: R 77 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8326 (ttpp) outliers start: 33 outliers final: 29 residues processed: 259 average time/residue: 0.7503 time to fit residues: 266.3426 Evaluate side-chains 269 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 234 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** R 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096261 restraints weight = 62357.696| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.15 r_work: 0.3147 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13938 Z= 0.169 Angle : 0.547 9.061 19075 Z= 0.275 Chirality : 0.044 0.161 2145 Planarity : 0.004 0.056 2317 Dihedral : 10.566 93.006 2232 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.83 % Allowed : 15.77 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1549 helix: 0.06 (0.30), residues: 334 sheet: -1.37 (0.23), residues: 476 loop : -0.40 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 22 HIS 0.008 0.001 HIS R 246 PHE 0.018 0.001 PHE R 170 TYR 0.014 0.001 TYR R 91 ARG 0.009 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7352.43 seconds wall clock time: 131 minutes 32.33 seconds (7892.33 seconds total)